Escherichia coli immunogens with improved solubility

ABSTRACT

Variants of the pathogenic  E. coli  ‘AcfD precursor’ have been identified with increased solubility as compared to the native AcfD protein that raise a substantially similar immune response in a subject as the native AcfD protein.

This application claims priority from (i) U.S. Provisional Application61/030902, filed 22 Feb. 2008 and (ii) Italian patent applicationMI2008A001249, filed 9 Jul. 2008, the contents of both of which areincorporated herein in full by reference.

TECHNICAL FIELD

This invention relates to immunisation against pathogenic Escherichiacoli strains.

BACKGROUND ART

E. coli strains have traditionally been classified as either commensalor pathogenic, and pathogenic strains are then sub-classified asintestinal or extraintestinal strains. Pathogenic E. coli are discussedin more detail in reference 1, and fall into a number of differentpathotypes i.e. a group of E. coli strains that cause a common diseaseusing a common set of virulence factors. Pathotyping of strains is aroutine technique that can be performed genotypically or phenotypically.One recent genotype-based pathotyping method [2] uses a DNA microarray.

Among intestinal strains at least six well-described pathotypes areknown: enteropathogenic (EPEC), enterohaemorrhagic (EHEC),enteroaggregative (EAEC), enteroinvasive (EIEC), enterotoxigenic (ETEC)and diffusely adherent (DAEC).

The extraintestinal pathogenic strains (or ‘ExPEC’ strains [3,4]) of E.coli include uropathogenic (UPEC) strains, neonatal meningitis (NMEC)strains, and septicemia-associated strains (SEPEC). ExPEC is the mostcommon cause of urinary tract infections and one of the leading causesof neonatal meningitis and neonatal sepsis in humans, which can lead toserious complications and death. Other types of extraintestinalinfections include osteomyelitis, pulmonary, intra-abdominal, softtissue, and intravascular device-associated infections. Another ExPECpathotype outside humans is avian pathogenic (APEC), causingextraintestinal infections in poultry.

Most previous ExPEC vaccines have been based on cell lysates or oncellular structures. SOLCOUROVAC™ includes ten different heat-killedbacteria including six ExPEC strains. URO-VAXOM™ is an oral tabletvaccine containing lyophilised bacterial lysates of 18 selected E. colistrains. Baxter Vaccines developed a UTI vaccine based on pili from 6 to10 different strains. MedImmune developed a product called MEDI 516based on the FimH adhesin complex. In contrast, references 5 and 6discloses specific immunogens from ExPEC strains that can be used as thebasis of defined vaccines against both NMEC and UPEC strains.

It is an object of the invention to provide further and better antigensfor use in immunisation against pathogenic E. coli strains, and moreparticularly against intestinal pathotypes (e.g. EAEC, EIEC, EPEC andETEC strains) as well as ExPEC pathotypes.

DISCLOSURE OF THE INVENTION

One of the many antigens disclosed in reference 5 is annotated as theaccessory colonization factor D (AcfD) precursor (SEQ ID NOs: 7051 &7052 therein; SEQ ID NOs: 1 & 2 herein). Reference 5 discloses thesequence from NMEC strain IHE3034, and the present invention is based onvariants of the ExPEC ‘AcfD precursor’ that have been identified infurther pathotypes, including APEC, UPEC, EAEC, EIEC, EPEC and ETECstrains. Unlike the disclosure of reference 5, these variants can beparticularly useful for treating intestinal pathotypes. Thus theinvention provides such variants, together with their use in immunisingpatients against E. coli infections. In addition, this disclosureincludes fragments of the AcfD protein of all E. coli pathotypes wherethe fragment has increased solubility as compared to the full lengthwhile raising a substantially similar immune response in a subject asthat raised by the full length protein.

Polypeptides Used with the Invention

The invention provides a polypeptide comprising an amino acid sequencethat:

-   -   (a) is identical (i.e. 100% identical) to any one of SEQ ID NOs        3 to 16;    -   (b) has at least a% sequence identity to one or more of SEQ ID        NOs 3 to 16;    -   (c) is a fragment of at least b consecutive amino acids of one        or more of SEQ ID NOs 3 to 16;    -   (d) has 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 (or more) single amino        acid alterations (deletions, insertions, substitutions), which        may be at separate locations or may be contiguous, as compared        to the sequences of (a) or (b); and/or    -   (e) when aligned with any one of SEQ ID NOs 3 to 16 using a        pairwise alignment algorithm, each moving window of x amino        acids from N-terminus to C-terminus (such that for an alignment        that extends to p amino acids, where p>x, there are p−x+1 such        windows) has at least x·y identical aligned amino acids, where:        x is selected from 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90,        100, 150, 200; y is selected from 0.50, 0.60, 0.70, 0.75, 0.80,        0.85, 0.90, 0.91, 0.92, 0.93, 0.94, 0.95, 0.96, 0.97, 0.98,        0.99; and if x·y is not an integer then it is rounded up to the        nearest integer. The preferred pairwise alignment algorithm is        the Needleman-Wunsch global alignment algorithm [7], using        default parameters (e.g. with Gap opening penalty=10.0, and with        Gap extension penalty=0.5, using the EBLOSUM62 scoring matrix).        This algorithm is conveniently implemented in the needle tool in        the EMBOSS package [8].

These polypeptides include variants of SEQ ID NOs 3 to 16, includingallelic variants, polymorphic forms, homologs, orthologs, paralogs,mutants, etc.

The value of a may be selected from 50%, 60%, 65%, 70%, 75%, 80%, 85%,87.5%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more.

The value of b may be selected from 7, 8, 9, 10, 12, 14, 16, 18, 20, 25,30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more. Preferredfragments of comprise an epitope or immunogenic fragment from SEQ ID NOs3 to 16. Other preferred fragments lack one or more amino acids (e.g. 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminusand/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15,20, 25 or more) from the N-terminus of SEQ ID NOs 3 to 16, preferablywhile retaining at least one epitope or immunogenic fragment of SEQ IDNOs 3 to 16. Other fragments omit one or more protein domains e.g.omission of a signal peptide, of a cytoplasmic domain, of atransmembrane domain, of an extracellular domain, etc. A deletion at theN-terminus, up to and including the GGGSG sequence (i.e. for SEQ ID NO:3, deletion of amino acids of amino acids 1 to 30), provides a usefulfragment (see, e.g., SEQ ID NOs 99-113. As demonstrated herein, suchdeletions increase the solubility of the AcfD polypeptide whileretaining substantially the same immunogenicity.

Another useful fragment of the invention is formed by cleavage of one ofSEQ ID NOs: 3 to 16 around its Arg-rich region (e.g. residues 770-775 ofSEQ ID NO: 3). For instance, one such fragment has, at or within 20amino acids of its C-terminus, a sequence having at least a% identity toamino acids 760-769 of SEQ ID NO: 3; another such fragment has, at orwithin 20 amino acids of its N-terminus, a sequence having at least a%identity to amino acids 776-785 of SEQ ID NO: 3. Fragments downstream ofthe Arg-rich region are particularly useful.

The invention also provides a polypeptide comprising an amino acidsequence that:

-   -   (a) is identical (i.e. 100% identical) to any one of SEQ ID NOs        3 to 16, SEQ ID NOs 99-113, or SEQ ID NOs 114-128;    -   (b) has at least a% sequence identity to one or more of SEQ ID        NOs 3 to 16, SEQ ID NOs 99-113, or SEQ ID NOs 114-128;    -   (c) is a fragment of at least b consecutive amino acids of one        or more of SEQ ID NOs 3 to 16, SEQ ID NOs 99-113, or SEQ ID NOs        114-128;    -   (d) has 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 (or more) single amino        acid alterations (deletions, insertions, substitutions), which        may be at separate locations or may be contiguous, as compared        to the sequences of (a) or (b); and/or    -   (e) when aligned with any one of SEQ ID NOs 3 to 16, SEQ ID NOs        99-113, or SEQ ID NOs 114-128 using a pairwise alignment        algorithm, each moving window of x amino acids from N-terminus        to C-terminus (such that for an alignment that extends to p        amino acids, where p>x, there are p−x+1 such windows) has at        least x·y identical aligned amino acids, where: x is selected        from 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200;        y is selected from 0.50, 0.60, 0.70, 0.75, 0.80, 0.85, 0.90,        0.91, 0.92, 0.93, 0.94, 0.95, 0.96, 0.97, 0.98, 0.99; and if x·y        is not an integer then it is rounded up to the nearest integer.        The preferred pairwise alignment algorithm is the        Needleman-Wunsch global alignment algorithm [9], using default        parameters (e.g. with Gap opening penalty=10.0, and with Gap        extension penalty=0.5, using the EBLOSUM62 scoring matrix). This        algorithm is conveniently implemented in the needle tool in the        EMBOSS package [10].

These polypeptides include variants of SEQ ID NOs 3 to 16, SEQ ID NOs99-113, and SEQ ID NOs 114-128, including allelic variants, polymorphicforms, homologs, orthologs, paralogs, mutants, etc.

The value of a may be selected from 50%, 60%, 65%, 70%, 75%, 80%, 85%,87.5%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more.

The value of b may be selected from 7, 8, 9, 10, 12, 14, 16, 18, 20, 25,30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more. Preferredfragments of comprise an epitope or immunogenic fragment from SEQ ID NOs3 to 16, SEQ ID NOs 99-113, and SEQ ID NOs 114-128. Other preferredfragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 15, 20, 25 or more) from the C-terminus and/or one or more aminoacids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from theN-terminus of SEQ ID NOs 3 to 16, SEQ ID NOs 99-113, or SEQ ID NOs114-128, preferably while retaining at least one epitope or immunogenicfragment of SEQ ID NOs 3 to 16, SEQ ID NOs 99-113, or SEQ ID NOs114-128. Other fragments omit one or more protein domains e.g. omissionof a signal peptide, of a cytoplasmic domain, of a transmembrane domain,of an extracellular domain, etc. A deletion at the N-terminus, up to andincluding the GGGSG sequence (i.e. for SEQ ID NO: 3, deletion of aminoacids of amino acids 1 to 30), provides a useful fragment (see, e.g.,SEQ ID NOs 99-113. Deletion of about 90 amino acids at the N-terminus,to remove the proline-rich region, is also useful (see, e.g., SEQ ID NOs114-128). As demonstrated herein, such deletions increase the solubilityof the AcfD polypeptide while retaining substantially the sameimmunogenicity.

An epitope within a fragment may be a B-cell epitope and/or a T-cellepitope. Such epitopes can be identified empirically (e.g. using PEPSCAN[11,12] or similar methods), or they can be predicted (e.g. using theJameson-Wolf antigenic index [13], matrix-based approaches [14],MAPITOPE [15], TEPITOPE [16,17], neural networks [18], OptiMer & EpiMer[19, 20], ADEPT [21], Tsites [22], hydrophilicity [23], antigenic index[24] or the methods disclosed in references 25-29, etc.). Epitopes arethe parts of an antigen that are recognised by and bind to the antigenbinding sites of antibodies or T-cell receptors, and they may also bereferred to as “antigenic determinants”.

Immunogenic fragments of SEQ ID NOs 3 to 16 discussed above include,without limitation, immunogenic fragments that, when administered to asubject in a suitable composition which can include an adjuvant(including without limitation any of the adjuvants listed or discussedin the section “Immunogenic compositions and medicaments” below), or asuitable carrier coupled to the polypeptide, induces an antibody orT-cell mediated immune response that recognizes the isolated full lengthpolypeptide SEQ ID NOs 3 to 16, respectively, from which the immunogenicfragment is derived.

Particularly useful fragments include, but are not limited to, SEQ IDNOs: 17 to 95.

Immunogenic fragments of SEQ ID NOs 3 to 16, SEQ ID NOs 99-113, or SEQID NOs 114-128 discussed above include, without limitation, immunogenicfragments that, when administered to a subject in a suitable compositionwhich can include an adjuvant (including without limitation any of theadjuvants listed or discussed in the section “Immunogenic compositionsand medicaments” below), or a suitable carrier coupled to thepolypeptide, induces an antibody or T-cell mediated immune response thatrecognizes the isolated full length polypeptide SEQ ID NOs 3 to 16, SEQID NOs 99-113, or SEQ ID NOs 114-128, respectively, from which theimmunogenic fragment is derived.

Immunogenic fragments of SEQ ID NOs 3 to 16, SEQ ID NOs 99-113, or SEQID NOs 114-131, SEQ ID NOs 133-135, or SEQ ID NOs 137-139 include,without limitation, immunogenic fragments that, when administered to asubject in a suitable composition which can include an adjuvant(including without limitation any of the adjuvants listed or discussedin the section “Immunogenic compositions and medicaments” below), or asuitable carrier coupled to the polypeptide, induces an antibody orT-cell mediated immune response that recognizes the isolated full lengthpolypeptide SEQ ID NOs 3 to 16, SEQ ID NOs 99-113, or SEQ ID NOs114-131, SEQ ID NOs 133-135, or SEQ ID NOs 137-139, respectively, fromwhich the immunogenic fragment is derived.

A polypeptide of the invention may, compared to any one of SEQ ID NOs 3to 16, include one or more (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, etc.) aminoacid substitutions, such as conservative substitutions (i.e.substitutions of one amino acid with another which has a related sidechain). Genetically-encoded amino acids are generally divided into fourfamilies: (1) acidic i.e. aspartate, glutamate; (2) basic i.e. lysine,arginine, histidine; (3) non-polar i.e. alanine, valine, leucine,isoleucine, proline, phenylalanine, methionine, tryptophan; and (4)uncharged polar i.e. glycine, asparagine, glutamine, cysteine, serine,threonine, tyrosine. Phenylalanine, tryptophan, and tyrosine aresometimes classified jointly as aromatic amino acids. In general,substitution of single amino acids within these families does not have amajor effect on the biological activity.

A polypeptide of the invention may also, compared to any one of SEQ IDNOs 3 to 16, SEQ ID NOs 99-113, or SEQ ID NOs 114-128, include one ormore (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, etc.) amino acid substitutions,such as conservative substitutions (i.e. substitutions of one amino acidwith another which has a related side chain). Genetically-encoded aminoacids are generally divided into four families: (1) acidic i.e.aspartate, glutamate; (2) basic i.e. lysine, arginine, histidine; (3)non-polar i.e. alanine, valine, leucine, isoleucine, proline,phenylalanine, methionine, tryptophan; and (4) uncharged polar i.e.glycine, asparagine, glutamine, cysteine, serine, threonine, tyrosine.Phenylalanine, tryptophan, and tyrosine are sometimes classified jointlyas aromatic amino acids. In general, substitution of single amino acidswithin these families does not have a major effect on the biologicalactivity.

A polypeptide of the invention may additionally, compared to any one ofSEQ ID NOs 3 to 16, SEQ ID NOs 99-113, SEQ ID NOs 114-128, SEQ ID NOs129-131 SEQ ID NOs 133-135, or SEQ ID NOs 137-139, include one or more(e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, etc.) amino acid substitutions, such asconservative substitutions (i.e. substitutions of one amino acid withanother which has a related side chain). Genetically-encoded amino acidsare generally divided into four families: (1) acidic i.e. aspartate,glutamate; (2) basic i.e. lysine, arginine, histidine; (3) non-polari.e. alanine, valine, leucine, isoleucine, proline, phenylalanine,methionine, tryptophan; and (4) uncharged polar i.e. glycine,asparagine, glutamine, cysteine, serine, threonine, tyrosine.Phenylalanine, tryptophan, and tyrosine are sometimes classified jointlyas aromatic amino acids. In general, substitution of single amino acidswithin these families does not have a major effect on the biologicalactivity.

A polypeptide may include one or more (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9,etc.) single amino acid deletions relative to any one of SEQ ID NOs 3 to16. Similarly, a polypeptides may include one or more (e.g. 1, 2, 3, 4,5, 6, 7, 8, 9, etc.) insertions (e.g. each of 1, 2, 3, 4 or 5 aminoacids) relative to any one of SEQ ID NOs 3 to 16.

A polypeptide may also include one or more (e.g. 1, 2, 3, 4, 5, 6, 7, 8,9, etc.) single amino acid deletions relative to any one of SEQ ID NOs 3to 16, SEQ ID NOs 99-113, or SEQ ID NOs 114-128. Similarly, apolypeptides may include one or more (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9,etc.) insertions (e.g. each of 1, 2, 3, 4 or 5 amino acids) relative toany one of SEQ ID NOs 3 to 16.

A polypeptide may additionally include one or more (e.g. 1, 2, 3, 4, 5,6, 7, 8, 9, etc.) single amino acid deletions relative to any one of SEQID NOs 3 to 16, SEQ ID NOs 99-113, or SEQ ID NOs 114-128, SEQ ID NOs129-131, SEQ ID NOs 133-135, or SEQ ID NOs 137-139. Similarly, apolypeptides may include one or more (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9,etc.) insertions (e.g. each of 1, 2, 3, 4 or 5 amino acids) relative toany one of SEQ ID NOs 3 to 16, 129, 133, or 137.

Within group (c) of either of the above, deletions or substitutions maybe at the N-terminus and/or C-terminus, or may be between the twotermini. Thus a truncation is an example of a deletion. Truncations mayinvolve deletion of up to 40 (or more) amino acids at the N-terminusand/or C-terminus. As mentioned above, for instance, truncation toremove the N-terminus up to the GGGSG sequence can be used.

In general, when a polypeptide of the invention comprises a sequencethat is not identical to a complete one of SEQ ID NOs 3 to 16 (e.g. whenit comprises a sequence with <100% sequence identity thereto, or when itcomprises a fragment thereof) it is preferred that the polypeptide canelicit an antibody that recognises a polypeptide consisting of thecomplete SEQ ID sequence i.e. the antibody binds to one or more of saidSEQ ID NOs 3 to 16. Such antibody may bind specifically to SEQ ID NOs 3to 16, respectively while not binding to non-AcfD proteins with affinitysignificantly higher than the antibody's non-specific affinity to humanserum albumin as a non-specific binding reference standard.

Similarly, when a polypeptide of the invention comprises a sequence thatis not identical to a complete one of SEQ ID NOs 3 to 16, SEQ ID NOs99-113, or SEQ ID NOs 114-128 (e.g. when it comprises a sequence with<100% sequence identity thereto, or when it comprises a fragmentthereof) it is preferred that the polypeptide can elicit an antibodythat recognises a polypeptide consisting of the complete SEQ ID sequencei.e. the antibody binds to one or more of said SEQ ID NOs 3 to 16, SEQID NOs 99-113, or SEQ ID NOs 114-128. Such antibody may bindspecifically to SEQ ID NOs 3 to 16, SEQ ID NOs 99-113, or SEQ ID NOs114-128, respectively while not binding to non-AcfD proteins withaffinity significantly higher than the antibody's non-specific affinityto human serum albumin as a non-specific binding reference standard.

Additionally, when a polypeptide of the invention comprises a sequencethat is not identical to a complete one of SEQ ID NOs 3 to 16, SEQ IDNOs 99-113, SEQ ID NOs 114-128, SEQ ID NOs 129-131 SEQ ID NOs 133-135,or SEQ ID NOs 137-139 (e.g. when it comprises a sequence with <100%sequence identity thereto, or when it comprises a fragment thereof) itis preferred that the polypeptide can elicit an antibody that recognisesa polypeptide consisting of the complete SEQ ID sequence i.e. theantibody binds to one or more of said SEQ ID NOs 3 to 16, SEQ ID NOs99-113,

SEQ ID NOs 114-128, SEQ ID NOs 129-131, SEQ ID NOs 133-135, or SEQ IDNOs 137-139. Such antibody may bind specifically to SEQ ID NOs 3 to 16,SEQ ID NOs 99-113, SEQ ID NOs 114-128, SEQ ID NOs 129-131 SEQ ID NOs133-135, or SEQ ID NOs 137-139, respectively while not binding tonon-AcfD proteins with affinity significantly higher than the antibody'snon-specific affinity to human serum albumin as a non-specific bindingreference standard.

In one embodiment, the invention provides a polypeptide comprising anamino acid sequence: (a) having at least a% identity to any one of SEQID NOs 3 to 16; and (b) comprising a fragment of at least b consecutiveamino acids of said SEQ ID.

In another embodiment, the invention provides a polypeptide comprisingan amino acid sequence: (a) having at least a% identity to any one ofSEQ ID NOs 3 to 16, SEQ ID NOs 99-113, or SEQ ID NOs 114-128; and (b)comprising a fragment of at least b consecutive amino acids of said SEQID.

In yet another embodiment, the invention provides a polypeptidecomprising an amino acid sequence: (a) having at least a% identity toany one of SEQ ID NOs 3 to 16, SEQ ID NOs 99-113, SEQ ID NOs 114-128,SEQ ID NOs 129-131, SEQ ID NOs 133-135, or SEQ ID NOs 137-139; and (b)comprising a fragment of at least b consecutive amino acids of said SEQID.

A polypeptide of the invention may include a metal ion e.g. a metal ionthat is coordinated by one or more amino acids in the polypeptide chain.For instance, the polypeptide may include a monovalent, divalent ortrivalent metal cation. Divalent cations are typical, such as Mn²⁺,Fe²⁺, Co²⁺, Ni²⁺, Cu²⁺, etc. The divalent cation is preferably Zn²⁺. Theion may be coordinated by a HEAGH or HEVGH amino acid sequence.

Polypeptides used with the invention can take various forms (e.g.native, fusions, glycosylated, non-glycosylated, lipidated,non-lipidated, phosphorylated, non-phosphorylated, myristoylated,non-myristoylated, monomeric, multimeric, particulate, denatured, etc.).For instance, a polypeptide of the invention may have a lipidatedN-terminal cysteine (e.g. Cys-24 of SEQ ID NOs: 3 to 16). Polypeptidesused with the invention can be prepared by various means (e.g.recombinant expression, purification from cell culture, chemicalsynthesis, etc.). Recombinantly-expressed proteins are preferred.

Polypeptides used with the invention are preferably provided in purifiedor substantially purified form i.e. substantially free from otherpolypeptides (e.g. free from naturally-occurring polypeptides),particularly from other E. coli or host cell polypeptides, and aregenerally at least about 50% pure (by weight), and usually at leastabout 90% pure i.e. less than about 50%, and more preferably less thanabout 10% (e.g. 5%) of a composition is made up of other expressedpolypeptides. Thus the antigens in the compositions are separated fromthe whole organism with which the molecule is expressed.

Polypeptides used with the invention are preferably E. colipolypeptides. Such polypeptides may be further selected from NMEC, APEC,UPEC, EAEC, EIEC, EPEC and ETEC E. coli polypeptides.

The term “polypeptide” refers to amino acid polymers of any length. Thepolymer may be linear or branched, it may comprise modified amino acids,and it may be interrupted by non-amino acids. The terms also encompassan amino acid polymer that has been modified naturally or byintervention; for example, disulfide bond formation, glycosylation,lipidation, acetylation, phosphorylation, or any other manipulation ormodification, such as conjugation with a labeling component. Alsoincluded are, for example, polypeptides containing one or more analogsof an amino acid (including, for example, unnatural amino acids, etc.),as well as other modifications known in the art. Polypeptides can occuras single chains or associated chains.

The invention provides polypeptides comprising a sequence -P-Q- or-Q-P-, wherein: -P- is an amino acid sequence as defined above and -Q-is not a sequence as defined above i.e. the invention provides fusionproteins. Where the N-terminus codon of -P- is not ATG, but this codonis not present at the N-terminus of a polypeptide, it will be translatedas the standard amino acid for that codon rather than as a Met. Wherethis codon is at the N-terminus of a polypeptide, however, it will betranslated as Met. Examples of -Q- moieties include, but are not limitedto, histidine tags (i.e. His_(n) where n=3, 4, 5, 6, 7, 8, 9, 10 ormore), a maltose-binding protein, or glutathione-S-transferase (GST).

The invention also provides an oligomeric protein comprising apolypeptide of the invention. The oligomer may be a dimer, a trimer, atetramer, etc. The oligomer may be a homo-oligomer or a hetero-oligomer.Polypeptides in the oligomer may be covalently or non-covalentlyassociated.

The invention also provides E. coli polypeptides which are fragments ofthe full length AcfD (of which SEQ ID NOs 2-16 are representativeexamples) which have increased solubility over the full length proteinwhile raising a substantially similar immune response in a subject asthat raised by the full length protein. Examples of such immunogenicpolypeptide fragments include any of SEQ ID NOs 99-128. Increasedsolubility may be measured by any means available to one of skill in theart. One simple method involves overexpression of the fragment inbacteria and running comparative samples of total bacterial lysateversus bacterial lysate supernatant after centrifugation or samples ofbacterial lysate pellet after centrifugation versus samples of bacteriallysate supernatant after centrifugation. One of skill in the art wouldgrow and express such immunogenic polypeptide fragments using standardtechniques (e.g., transform BL21(DE3) bacteria with a pET21 expressionvector expressing the fragment, grow the bacteria to 0.6 OD₆₀₀ in LB andinduce with 1 mM IPTG, and culture for 3 hours after induction), Suchsamples may be run on SDS PAGE (e.g., 4-12% MOPS) and roughly quantifiedby scanning the resulting stained gel and measuring the relative size ofthe bands. The increased solubility as used herein is as determined at25° C. Such increased solubility can be a 10% increase in solublepolypeptide, a 20% increase in soluble polypeptide, a 30% increase insoluble polypeptide, a 50% increase in soluble polypeptide, a 75%increase in soluble polypeptide, a 100% increase (i.e., two-fold) insoluble polypeptide, a three-fold increase in soluble polypeptide, afour-fold increase in soluble polypeptide, a five-fold increase insoluble polypeptide, a seven-fold increase in soluble polypeptide, or aten-fold increase in soluble polypeptide.

The invention additional provides E. coli polypeptides that arefragments of less than the full length AcfD (of which SEQ ID NOs 2-16are representative examples). These less than full length fragment haveincreased solubility as compare to the full length protein while raisinga substantially similar immune response in a subject as compared to thatraised by the full length protein. Examples of such immunogenicpolypeptide fragments include any of SEQ ID NOs 99-128. Increasedsolubility may be measured by any means available to one of skill in theart. One simple method involves overexpression of the fragment inbacteria and running comparative samples of total bacterial lysateversus bacterial lysate supernatant after centrifugation or samples ofbacterial lysate pellet after centrifugation versus samples of bacteriallysate supernatant after centrifugation. One of skill in the art wouldgrow and express such immunogenic polypeptide fragments using standardtechniques (e.g., transform BL21(DE3) bacteria with a pET21 expressionvector expressing the fragment, grow the bacteria to 0.6 OD₆₀₀ in LB andinduce with 1 mM IPTG, and culture for 3 hours after induction). Suchsamples may be run on SDS PAGE (e.g., 4-12% MOPS) and roughly quantifiedby scanning the resulting stained gel and measuring the relative size ofthe bands. The increased solubility as used herein is as determined at25° C. Such increased solubility can be a 10% increase in solublepolypeptide, a 20% increase in soluble polypeptide, a 30% increase insoluble polypeptide, a 50% increase in soluble polypeptide, a 75%increase in soluble polypeptide, a 100% increase (i.e., two-fold) insoluble polypeptide, a three-fold increase in soluble polypeptide, afour-fold increase in soluble polypeptide, a five-fold increase insoluble polypeptide, a seven-fold increase in soluble polypeptide, or aten-fold increase in soluble polypeptide in each case as comparedbetween the less than full length polypeptide compared to thecorresponding full length protein measured under the same conditions.

The invention additional provides E. coli polypeptides that arefragments of less than the full length AcfD (of which SEQ ID NOs 2-16,129, 133, and 137 are representative examples). These less than fulllength fragment have increased solubility as compare to the full lengthprotein while raising a substantially similar immune response in asubject as compared to that raised by the full length protein. Examplesof such immunogenic polypeptide fragments include any of SEQ ID NOs99-128, SEQ ID NOs 130-131, SED ID NOs 134-135, and SEQ ID NOs 138-139.Increased solubility may be measured by any means available to one ofskill in the art. One simple method involves overexpression of thefragment in bacteria and running comparative samples of total bacteriallysate versus bacterial lysate supernatant after centrifugation orsamples of bacterial lysate pellet after centrifugation versus samplesof bacterial lysate supernatant after centrifugation. One of skill inthe art would grow and express such immunogenic polypeptide fragmentsusing standard techniques (e.g., transform BL21(DE3) bacteria with apET21 expression vector expressing the fragment, grow the bacteria to0.6 OD₆₀₀ in LB and induce with 1 mM IPTG, and culture for 3 hours afterinduction). Such samples may be run on SDS PAGE (e.g., 4-12% MOPS) androughly quantified by scanning the resulting stained gel and measuringthe relative size of the bands. The increased solubility as used hereinis as determined at 25° C. Such increased solubility can be a 10%increase in soluble polypeptide, a 20% increase in soluble polypeptide,a 30% increase in soluble polypeptide, a 50% increase in solublepolypeptide, a 75% increase in soluble polypeptide, a 100% increase(i.e., two-fold) in soluble polypeptide, a three-fold increase insoluble polypeptide, a four-fold increase in soluble polypeptide, afive-fold increase in soluble polypeptide, a seven-fold increase insoluble polypeptide, or a ten-fold increase in soluble polypeptide ineach case as compared between the less than full length polypeptidecompared to the corresponding full length protein measured under thesame conditions.

Comparison of the immune response raised in a subject by the polypeptidewith the immune response raised by the full length protein may becarried out use by any means available to one of skill in the art. Onesimple method as used in the examples below involves immunization of amodel subject such as mouse and then challenge with a lethal dose of E.coli. For proper comparison, one of skill in the art would naturallyselect the same adjuvant such as Freund's complete adjuvant. In such atest the immunogenic polypeptide fragments of the present invention willraise a substantially similar immune response in a subject (i.e., willprovide substantially the same protection against the lethal challenge)if, for example, the polypeptide provides at least 70% of the protectionprovided by the full length protein, at least 80% of the protectionprovided by the full length protein, at least 85% of the protectionprovided by the full length protein, at least 90% of the protectionprovided by the full length protein, at least 95% of the protectionprovided by the full length protein, at least 97% of the protectionprovided by the full length protein, at least 98% of the protectionprovided by the full length protein, or at least 99% of the protectionprovided by the full length protein.

Furthermore, comparison between the immune response raised in a subjectby the less than full length polypeptide and the immune response raisedby the corresponding full length protein may be carried out use by anymeans available to one of skill in the art. One simple method as used inthe examples below involves immunization of a model subject such asmouse and then challenge with a lethal dose of E. coli. For propercomparison, one of skill in the art would naturally select the sameadjuvant such as Freund's complete adjuvant. In such a test theimmunogenic less than full length polypeptide fragments of the presentinvention will raise a substantially similar immune response in asubject as compared to the immune response raised by the correspondingfull length protein (i.e., will provide substantially the sameprotection against the lethal challenge) if, for example, thepolypeptide provides at least 70% of the protection provided by the fulllength protein, at least 80% of the protection provided by the fulllength protein, at least 85% of the protection provided by the fulllength protein, at least 90% of the protection provided by the fulllength protein, at least 95% of the protection provided by the fulllength protein, at least 97% of the protection provided by the fulllength protein, at least 98% of the protection provided by the fulllength protein, or at least 99% of the protection provided by the fulllength protein.

The full length AcfD protein against which the immunogenic polypeptidefragment would be compared (for both solubility and immune responseraised) may be any representative E. coli AcfD protein including withoutlimitation SEQ ID NOs 2-16. In preferred embodiments, the AcfD proteinwill be the corresponding full length protein from which the immunogenicpolypeptide fragment is obtained.

In some embodiments, the immunogenic polypeptide will contain a deletionrelative to the E. coli AcfD protein which results in the increasedsolubility. The deletion may include removal of substantially all of theN-terminal amino acids up to the gly-ser linker or gly-ser region,removal of all or a part of the N-terminal proline-rich repeat, or both.One of skill in the art would understand the N-terminal amino acids upto the gly-ser linker or gly-ser region to correspond to the region ofthe E. coli AcfD protein of interest to be that portion of the proteinthat aligns to the region of the E. coli AcfD proteins identified hereinwhich are denoted with a “G” under the alignment in FIG. 1. Similarly,one of skill in the art would understand the N-terminal proline-richrepeat to correspond to the region of the E. coli AcfD protein ofinterest to be that portion of the protein that aligns to the region ofthe E. coli AcfD proteins identified herein which are denoted with a “P”under the alignment in FIG. 1.

In certain aspects, the immunogenic polypeptide fragment may be afragment which comprises SEQ ID NOs 99 or 114 (including any fragmentencompassing SEQ ID NO: 114 with an N-terminus between the N-terminus ofSEQ ID NOs 99 and 114) provided that the immunogenic polypeptidefragment does not have the amino acid sequence of SEQ ID NO 2. Theimmunogenic polypeptide fragment may be a fragment which comprises SEQID NOs 100 or 115 (including any fragment encompassing SEQ ID NO: 115with an N-terminus between the N-terminus of SEQ ID NOs 100 and 115)provided that the immunogenic polypeptide fragment does not have theamino acid sequence of SEQ ID NO 3. The immunogenic polypeptide fragmentmay be a fragment which comprises SEQ ID NOs 101 or 116 (including anyfragment encompassing SEQ ID NO: 116 with an N-terminus between theN-terminus of SEQ ID NOs 101 and 116) provided that the immunogenicpolypeptide fragment does not have the amino acid sequence of SEQ ID NO4. The immunogenic polypeptide fragment may be a fragment whichcomprises SEQ ID NOs 102 or 117 (including any fragment encompassing SEQID NO: 117 with an N-terminus between the N-terminus of SEQ ID NOs 102and 117) provided that the immunogenic polypeptide fragment does nothave the amino acid sequence of SEQ ID NO 5. The immunogenic polypeptidefragment may be a fragment which comprises SEQ ID NOs 103 or 118(including any fragment encompassing SEQ ID NO: 118 with an N-terminusbetween the N-terminus of SEQ ID NOs 103 and 118) provided that theimmunogenic polypeptide fragment does not have the amino acid sequenceof SEQ ID NO 6. The immunogenic polypeptide fragment may be a fragmentwhich comprises SEQ ID NOs 104 or 119 (including any fragmentencompassing SEQ ID NO: 119 with an N-terminus between the N-terminus ofSEQ ID NOs 104 and 119) provided that the immunogenic polypeptidefragment does not have the amino acid sequence of SEQ ID NO 7. Theimmunogenic polypeptide fragment may be a fragment which comprises SEQID NOs 105 or 120 (including any fragment encompassing SEQ ID NO: 120with an N-terminus between the N-terminus of SEQ ID NOs 105 and 120)provided that the immunogenic polypeptide fragment does not have theamino acid sequence of SEQ ID NO 8. The immunogenic polypeptide fragmentmay be a fragment which comprises SEQ ID NOs 106 or 121 (including anyfragment encompassing SEQ ID NO: 121 with an N-terminus between theN-terminus of SEQ ID NOs 106 and 121) provided that the immunogenicpolypeptide fragment does not have the amino acid sequence of SEQ ID NO9. The immunogenic polypeptide fragment may be a fragment whichcomprises SEQ ID NOs 107 or 122 (including any fragment encompassing SEQID NO: 122 with an N-terminus between the N-terminus of SEQ ID NOs 107and 122) provided that the immunogenic polypeptide fragment does nothave the amino acid sequence of SEQ ID NO 10. The immunogenicpolypeptide fragment may be a fragment which comprises SEQ ID NOs 108 or123 (including any fragment encompassing SEQ ID NO: 123 with anN-terminus between the N-terminus of SEQ ID NOs 108 and 123) providedthat the immunogenic polypeptide fragment does not have the amino acidsequence of SEQ ID NO 11. The immunogenic polypeptide fragment may be afragment which comprises SEQ ID NOs 109 or 124 (including any fragmentencompassing SEQ ID NO: 124 with an N-terminus between the N-terminus ofSEQ ID NOs 109 and 124) provided that the immunogenic polypeptidefragment does not have the amino acid sequence of SEQ ID NO 12. Theimmunogenic polypeptide fragment may be a fragment which comprises SEQID NOs 110 or 125 (including any fragment encompassing SEQ ID NO: 125with an N-terminus between the N-terminus of SEQ ID NOs 110 and 125)provided that the immunogenic polypeptide fragment does not have theamino acid sequence of SEQ ID NO 13. The immunogenic polypeptidefragment may be a fragment which comprises SEQ ID NOs 111 or 126(including any fragment encompassing SEQ ID NO: 126 with an N-terminusbetween the N-terminus of SEQ ID NOs 111 and 126) provided that theimmunogenic polypeptide fragment does not have the amino acid sequenceof SEQ ID NO 14. The immunogenic polypeptide fragment may be a fragmentwhich comprises SEQ ID NOs 112 or 127 (including any fragmentencompassing SEQ ID NO: 127 with an N-terminus between the N-terminus ofSEQ ID NOs 112 and 127) provided that the immunogenic polypeptidefragment does not have the amino acid sequence of SEQ ID NO 15. Theimmunogenic polypeptide fragment may be a fragment which comprises SEQID NOs 113 or 128 (including any fragment encompassing SEQ ID NO: 128with an N-terminus between the N-terminus of SEQ ID NOs 113 and 128)provided that the immunogenic polypeptide fragment does not have theamino acid sequence of SEQ ID NO 16. Any of the foregoing immunogenicpolypeptide fragments may also include variations so long as thevariations do not result in the immunogenic polypeptide having thesequence of any full length AcfD protein, including without limitationany of the variations listed in this section “Polypeptides used with theinvention.” Examples include: from 1 to 10 single amino acid alterationscompared to the applicable SEQ ID NOs; at least 85% sequence identity tothe applicable SEQ ID NOs; a fragment of at least 10 consecutive aminoacids of the applicable SEQ ID NOs; and when aligned with the applicableSEQ ID NOs using a pairwise alignment algorithm, each moving window of xamino acids from N terminus to C terminus has at least x·y identicalaligned amino acids, where x is 30 and y is 0.75.

The invention also provides a process for producing a polypeptide of theinvention, comprising the step of culturing a host cell transformed withnucleic acid of the invention under conditions which induce polypeptideexpression. The polypeptide may then be purified e.g. from culturesupernatants.

The invention provides an E. coli cell, containing a plasmid thatencodes a polypeptide of the invention. The chromosome of the E. colicell may include a homolog of AcfD, or such a homolog may be absent, butin both cases the polypeptide of the invention can be expressed from theplasmid. The plasmid may include a gene encoding a marker, etc. Theseand other details of suitable plasmids are given below.

Although expression of the polypeptides of the invention may take placein an E. coli strain, the invention will usually use a heterologous hostfor expression. The heterologous host may be prokaryotic (e.g. abacterium) or eukaryotic. Suitable hosts include, but are not limitedto, Bacillus subtilis, Vibrio cholerae, Salmonella typhi, Salmonellatyphimurium, Neisseria lactamica, Neisseria cinerea, Mycobacteria (e.g.M. tuberculosis), yeasts, etc.

The invention provides a process for producing a polypeptide of theinvention, comprising the step of synthesising at least part of thepolypeptide by chemical means.

Any and all of the foregoing proteins, polypeptides, hybridpolypeptides, epitopes and immunogenic fragments may be in any one of anumber of forms including, without limitation, recombinant, isolated orsubstantially purified (from materials co-existing with such proteins,polypeptides, hybrid polypeptides, epitopes and immunogenic fragments intheir natural state).

Nucleic Acids

The invention also provides nucleic acid encoding polypeptides andhybrid polypeptides of the invention. It also provides nucleic acidcomprising a nucleotide sequence that encodes one or more polypeptidesor hybrid polypeptides of the invention.

The invention also provides nucleic acid comprising nucleotide sequenceshaving sequence identity to such nucleotide sequences. Identity betweensequences is preferably determined by the Smith-Waterman homology searchalgorithm as described above. Such nucleic acids include those usingalternative codons to encode the same amino acid.

The invention also provides nucleic acid which can hybridize to thesenucleic acids. Hybridization reactions can be performed under conditionsof different “stringency”. Conditions that increase stringency of ahybridization reaction of widely known and published in the art (e.g.page 7.52 of reference 224). Examples of relevant conditions include (inorder of increasing stringency): incubation temperatures of 25° C., 37°C., 50° C., 55° C. and 68° C.; buffer concentrations of 10×SSC, 6×SSC,1×SSC, 0.1×SSC (where SSC is 0.15 M NaCl and 15 mM citrate buffer) andtheir equivalents using other buffer systems; formamide concentrationsof 0%, 25%, 50%, and 75%; incubation times from 5 minutes to 24 hours;1, 2, or more washing steps; wash incubation times of 1, 2, or 15minutes; and wash solutions of 6×SSC, 1×SSC, 0.1×SSC, or de-ionizedwater. Hybridization techniques and their optimization are well known inthe art (e.g. see refs 30, 31, 224, 226, etc.].

In some embodiments, nucleic acid of the invention hybridizes to atarget under low stringency conditions; in other embodiments ithybridizes under intermediate stringency conditions; in preferredembodiments, it hybridizes under high stringency conditions. Anexemplary set of low stringency hybridization conditions is 50° C. and10×SSC. An exemplary set of intermediate stringency hybridizationconditions is 55° C. and 1×SSC. An exemplary set of high stringencyhybridization conditions is 68° C. and 0.1×SSC.

The invention includes nucleic acid comprising sequences complementaryto these sequences (e.g. for antisense or probing, or for use asprimers).

Nucleic acids of the invention can be used in hybridisation reactions(e.g. Northern or Southern blots, or in nucleic acid microarrays or‘gene chips’) and amplification reactions (e.g. PCR, SDA, SSSR, LCR,TMA, NASBA, etc.) and other nucleic acid techniques.

Nucleic acid according to the invention can take various forms (e.g.single-stranded, double-stranded, vectors, primers, probes, labelledetc.). Nucleic acids of the invention may be circular or branched, butwill generally be linear. Unless otherwise specified or required, anyembodiment of the invention that utilizes a nucleic acid may utilizeboth the double-stranded form and each of two complementarysingle-stranded forms which make up the double-stranded form. Primersand probes are generally single-stranded, as are antisense nucleicacids.

Nucleic acids of the invention are preferably provided in purified orsubstantially purified form i.e. substantially free from other nucleicacids (e.g. free from naturally-occurring nucleic acids), particularlyfrom other E. coli or host cell nucleic acids, generally being at leastabout 50% pure (by weight), and usually at least about 90% pure. Nucleicacids of the invention are preferably E. coli nucleic acids.

Nucleic acids of the invention may be prepared in many ways e.g. bychemical synthesis (e.g. phosphoramidite synthesis of DNA) in whole orin part, by digesting longer nucleic acids using nucleases (e.g.restriction enzymes), by joining shorter nucleic acids or nucleotides(e.g. using ligases or polymerases), from genomic or cDNA libraries,etc.

Nucleic acid of the invention may be attached to a solid support (e.g. abead, plate, filter, film, slide, microarray support, resin, etc.).Nucleic acid of the invention may be labelled e.g. with a radioactive orfluorescent label, or a biotin label. This is particularly useful wherethe nucleic acid is to be used in detection techniques e.g. where thenucleic acid is a primer or as a probe.

The term “nucleic acid” includes in general means a polymeric form ofnucleotides of any length, which contain deoxyribonucleotides,ribonucleotides, and/or their analogs. It includes DNA, RNA, DNA/RNAhybrids. It also includes DNA or RNA analogs, such as those containingmodified backbones (e.g. peptide nucleic acids (PNAs) orphosphorothioates) or modified bases. Thus the invention includes mRNA,tRNA, rRNA, ribozymes, DNA, cDNA, recombinant nucleic acids, branchednucleic acids, plasmids, vectors, probes, primers, etc.. Where nucleicacid of the invention takes the form of RNA, it may or may not have a 5′cap.

Nucleic acids of the invention may be part of a vector i.e. part of anucleic acid construct designed for transduction/transfection of one ormore cell types. Vectors may be, for example, “cloning vectors” whichare designed for isolation, propagation and replication of insertednucleotides, “expression vectors” which are designed for expression of anucleotide sequence in a host cell, “viral vectors” which is designed toresult in the production of a recombinant virus or virus-like particle,or “shuttle vectors”, which comprise the attributes of more than onetype of vector. Preferred vectors are plasmids, as mentioned above. A“host cell” includes an individual cell or cell culture which can be orhas been a recipient of exogenous nucleic acid. Host cells includeprogeny of a single host cell, and the progeny may not necessarily becompletely identical (in morphology or in total DNA complement) to theoriginal parent cell due to natural, accidental, or deliberate mutationand/or change. Host cells include cells transfected or infected in vivoor in vitro with nucleic acid of the invention.

Where a nucleic acid is DNA, it will be appreciated that “U” in a RNAsequence will be replaced by “T” in the DNA. Similarly, where a nucleicacid is RNA, it will be appreciated that “T” in a DNA sequence will bereplaced by “U” in the RNA.

The term “complement” or “complementary” when used in relation tonucleic acids refers to Watson-Crick base pairing. Thus the complementof C is G, the complement of G is C, the complement of A is T (or U),and the complement of T (or U) is A. It is also possible to use basessuch as I (the purine inosine) e.g. to complement pyrimidines (C or T).

Nucleic acids of the invention can be used, for example: to producepolypeptides; as hybridization probes for the detection of nucleic acidin biological samples; to generate additional copies of the nucleicacids; to generate ribozymes or antisense oligonucleotides; assingle-stranded DNA primers or probes; or as triple-strand formingoligonucleotides.

The invention provides a process for producing nucleic acid of theinvention, wherein the nucleic acid is synthesised in part or in wholeusing chemical means.

The invention provides vectors comprising nucleotide sequences of theinvention (e.g. cloning or expression vectors) and host cellstransformed with such vectors.

Nucleic acid amplification according to the invention may bequantitative and/or real-time.

For certain embodiments of the invention, nucleic acids are preferablyat least 7 nucleotides in length (e.g. 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 65, 70, 75, 80, 90, 100, 110,120, 130, 140, 150, 160, 170, 180, 190, 200, 225, 250, 275, 300nucleotides or longer).

For certain embodiments of the invention, nucleic acids are preferablyat most 500 nucleotides in length (e.g. 450, 400, 350, 300, 250, 200,150, 140, 130, 120, 110, 100, 90, 80, 75, 70, 65, 60, 55, 50, 45, 40,39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22,21, 20, 19, 18, 17, 16, 15 nucleotides or shorter).

Primers and probes of the invention, and other nucleic acids used forhybridization, are preferably between 10 and 30 nucleotides in length(e.g. 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, or 30 nucleotides).

Immunogenic Compositions and Medicaments

Polypeptides of the invention are useful as active ingredients(immunogens) in immunogenic compositions, and such compositions may beuseful as vaccines. Vaccines according to the invention may either beprophylactic (i.e. to prevent infection) or therapeutic (i.e. to treatinfection), but will typically be prophylactic.

Immunogenic compositions will be pharmaceutically acceptable. They willusually include components in addition to the antigens e.g. theytypically include one or more pharmaceutical carrier(s), excipient(s)and/or adjuvant(s). A thorough discussion of carriers and excipients isavailable in ref. 221. Thorough discussions of vaccine adjuvants areavailable in refs. 32 and 33.

Compositions will generally be administered to a mammal in aqueous form.Prior to administration, however, the composition may have been in anon-aqueous form. For instance, although some vaccines are manufacturedin aqueous form, then filled and distributed and administered also inaqueous form, other vaccines are lyophilised during manufacture and arereconstituted into an aqueous form at the time of use. Thus acomposition of the invention may be dried, such as a lyophilisedformulation.

The composition may include preservatives such as thiomersal or2-phenoxyethanol. It is preferred, however, that the vaccine should besubstantially free from (i.e. less than 5 μg/ml) mercurial material e.g.thiomersal-free. Vaccines containing no mercury are more preferred.Preservative-free vaccines are particularly preferred.

To improve thermal stability, a composition may include a temperatureprotective agent.

To control tonicity, it is preferred to include a physiological salt,such as a sodium salt. Sodium chloride (NaCl) is preferred, which may bepresent at between 1 and 20 mg/ml e.g. about 10±2 mg/ml NaCl. Othersalts that may be present include potassium chloride, potassiumdihydrogen phosphate, disodium phosphate dehydrate, magnesium chloride,calcium chloride, etc.

Compositions will generally have an osmolality of between 200 mOsm/kgand 400 mOsm/kg, preferably between 240-360 mOsm/kg, and will morepreferably fall within the range of 290-310 mOsm/kg.

Compositions may include one or more buffers. Typical buffers include: aphosphate buffer; a Tris buffer; a borate buffer; a succinate buffer; ahistidine buffer (particularly with an aluminum hydroxide adjuvant); ora citrate buffer. Buffers will typically be included in the 5-20 mMrange.

The pH of a composition will generally be between 5.0 and 8.1, and moretypically between 6.0 and 8.0 e.g. 6.5 and 7.5, or between 7.0 and 7.8.

The composition is preferably sterile. The composition is preferablynon-pyrogenic e.g. containing <1 EU (endotoxin unit, a standard measure)per dose, and preferably <0.1 EU per dose. The composition is preferablygluten free.

The composition may include material for a single immunisation, or mayinclude material for multiple immunisations (i.e. a ‘multidose’ kit).The inclusion of a preservative is preferred in multidose arrangements.As an alternative (or in addition) to including a preservative inmultidose compositions, the compositions may be contained in a containerhaving an aseptic adaptor for removal of material.

Human vaccines are typically administered in a dosage volume of about0.5 ml, although a half dose (i.e. about 0.25 ml) may be administered tochildren.

Immunogenic compositions of the invention may also comprise one or moreimmunoregulatory agents. Preferably, one or more of the immunoregulatoryagents include one or more adjuvants. The adjuvants may include a TH1adjuvant and/or a TH2 adjuvant, further discussed below.

Adjuvants which may be used in compositions of the invention include,but are not limited to:

A. Mineral-Containing Compositions

Mineral containing compositions suitable for use as adjuvants in theinvention include mineral salts, such as aluminium salts and calciumsalts (or mixtures thereof). Calcium salts include calcium phosphate(e.g. the “CAP” particles disclosed in ref. 34). Aluminum salts includehydroxides, phosphates, sulfates, etc., with the salts taking anysuitable form (e.g. gel, crystalline, amorphous, etc.). Adsorption tothese salts is preferred. The mineral containing compositions may alsobe formulated as a particle of metal salt [35].

The adjuvants known as aluminum hydroxide and aluminum phosphate may beused. These names are conventional, but are used for convenience only,as neither is a precise description of the actual chemical compoundwhich is present (e.g. see chapter 9 of reference 32). The invention canuse any of the “hydroxide” or “phosphate” adjuvants that are in generaluse as adjuvants. The adjuvants known as “aluminium hydroxide” aretypically aluminium oxyhydroxide salts, which are usually at leastpartially crystalline. The adjuvants known as “aluminium phosphate” aretypically aluminium hydroxyphosphates, often also containing a smallamount of sulfate (i.e. aluminium hydroxyphosphate sulfate). They may beobtained by precipitation, and the reaction conditions andconcentrations during precipitation influence the degree of substitutionof phosphate for hydroxyl in the salt.

A fibrous morphology (e.g. as seen in transmission electron micrographs)is typical for aluminium hydroxide adjuvants. The pI of aluminiumhydroxide adjuvants is typically about 11 i.e. the adjuvant itself has apositive surface charge at physiological pH. Adsorptive capacities ofbetween 1.8-2.6 mg protein per mg Al⁺⁺⁺ at pH 7.4 have been reported foraluminium hydroxide adjuvants.

Aluminium phosphate adjuvants generally have a PO₄/Al molar ratiobetween 0.3 and 1.2, preferably between 0.8 and 1.2, and more preferably0.95±0.1. The aluminium phosphate will generally be amorphous,particularly for hydroxyphosphate salts. A typical adjuvant is amorphousaluminium hydroxyphosphate with PO₄/Al molar ratio between 0.84 and0.92, included at 0.6 mg Al³⁺/ml. The aluminium phosphate will generallybe particulate (e.g. plate-like morphology as seen in transmissionelectron micrographs). Typical diameters of the particles are in therange 0.5-20 μm (e.g. about 5-10 μm) after any antigen adsorption.Adsorptive capacities of between 0.7-1.5 mg protein per mg Al⁺⁺⁺ at pH7.4 have been reported for aluminium phosphate adjuvants.

The point of zero charge (PZC) of aluminium phosphate is inverselyrelated to the degree of substitution of phosphate for hydroxyl, andthis degree of substitution can vary depending on reaction conditionsand concentration of reactants used for preparing the salt byprecipitation. PZC is also altered by changing the concentration of freephosphate ions in solution (more phosphate=more acidic PZC) or by addinga buffer such as a histidine buffer (makes PZC more basic). Aluminiumphosphates used according to the invention will generally have a PZC ofbetween 4.0 and 7.0, more preferably between 5.0 and 6.5 e.g. about 5.7.

Suspensions of aluminium salts used to prepare compositions of theinvention may contain a buffer (e.g. a phosphate or a histidine or aTris buffer), but this is not always necessary. The suspensions arepreferably sterile and pyrogen-free. A suspension may include freeaqueous phosphate ions e.g. present at a concentration between 1.0 and20 mM, preferably between 5 and 15 mM, and more preferably about 10 mM.The suspensions may also comprise sodium chloride.

The invention can use a mixture of both an aluminium hydroxide and analuminium phosphate. In this case there may be more aluminium phosphatethan hydroxide e.g. a weight ratio of at least 2:1 e.g. ≧5:1, ≧6:1,≧7:1, ≧8:1, ≧9:1, etc.

The concentration of Al⁺⁺⁺ in a composition for administration to apatient is preferably less than 10 mg/ml e.g. ≦5 mg/ml, ≦4 mg/ml, ≦3mg/ml, ≦2 mg/ml, ≦1 mg/ml, etc. A preferred range is between 0.3 and 1mg/ml. A maximum of 0.85 mg/dose is preferred.

B. Oil Emulsions

Oil emulsion compositions suitable for use as adjuvants in the inventioninclude squalene-water emulsions, such as MF59 [Chapter 10 of ref. 32;see also ref. 36] (5% Squalene, 0.5% Tween 80, and 0.5% Span 85,formulated into submicron particles using a microfluidizer). CompleteFreund's adjuvant (CFA) and incomplete Freund's adjuvant (IFA) may alsobe used.

Various oil-in-water emulsion adjuvants are known, and they typicallyinclude at least one oil and at least one surfactant, with the oil(s)and surfactant(s) being biodegradable (metabolisable) and biocompatible.The oil droplets in the emulsion are generally less than 5 μm indiameter, and ideally have a sub-micron diameter, with these small sizesbeing achieved with a microfluidiser to provide stable emulsions.Droplets with a size less than 220 nm are preferred as they can besubjected to filter sterilization.

The emulsion can comprise oils such as those from an animal (such asfish) or vegetable source. Sources for vegetable oils include nuts,seeds and grains. Peanut oil, soybean oil, coconut oil, and olive oil,the most commonly available, exemplify the nut oils. Jojoba oil can beused e.g. obtained from the jojoba bean. Seed oils include saffloweroil, cottonseed oil, sunflower seed oil, sesame seed oil and the like.In the grain group, corn oil is the most readily available, but the oilof other cereal grains such as wheat, oats, rye, rice, teff, triticaleand the like may also be used. 6-10 carbon fatty acid esters of glyceroland 1,2-propanediol, while not occurring naturally in seed oils, may beprepared by hydrolysis, separation and esterification of the appropriatematerials starting from the nut and seed oils. Fats and oils frommammalian milk are metabolizable and may therefore be used in thepractice of this invention. The procedures for separation, purification,saponification and other means necessary for obtaining pure oils fromanimal sources are well known in the art. Most fish containmetabolizable oils which may be readily recovered. For example, codliver oil, shark liver oils, and whale oil such as spermaceti exemplifyseveral of the fish oils which may be used herein. A number of branchedchain oils are synthesized biochemically in 5-carbon isoprene units andare generally referred to as terpenoids. Shark liver oil contains abranched, unsaturated terpenoids known as squalene, 2,6,10,15,19,23-hexamethyl-2,6,10,14,18,22-tetracosahexaene, which is particularlypreferred herein. Squalane, the saturated analog to squalene, is also apreferred oil. Fish oils, including squalene and squalane, are readilyavailable from commercial sources or may be obtained by methods known inthe art. Other preferred oils are the tocopherols (see below). Mixturesof oils can be used.

Surfactants can be classified by their ‘HLB’ (hydrophile/lipophilebalance). Preferred surfactants of the invention have a HLB of at least10, preferably at least 15, and more preferably at least 16. Theinvention can be used with surfactants including, but not limited to:the polyoxyethylene sorbitan esters surfactants (commonly referred to asthe Tweens), especially polysorbate 20 and polysorbate 80; copolymers ofethylene oxide (EO), propylene oxide (PO), and/or butylene oxide (BO),sold under the DOWFAX™ tradename, such as linear EO/PO block copolymers;octoxynols, which can vary in the number of repeating ethoxy(oxy-1,2-ethanediyl) groups, with octoxynol-9 (Triton X-100, ort-octylphenoxypolyethoxyethanol) being of particular interest;(octylphenoxy)polyethoxyethanol (IGEPAL CA-630/NP-40); phospholipidssuch as phosphatidylcholine (lecithin); nonylphenol ethoxylates, such asthe Tergitol™ NP series; polyoxyethylene fatty ethers derived fromlauryl, cetyl, stearyl and oleyl alcohols (known as Brij surfactants),such as triethyleneglycol monolauryl ether (Brij 30); and sorbitanesters (commonly known as the SPANs), such as sorbitan trioleate (Span85) and sorbitan monolaurate. Non-ionic surfactants are preferred.Preferred surfactants for including in the emulsion are Tween 80(polyoxyethylene sorbitan monooleate), Span 85 (sorbitan trioleate),lecithin and Triton X-100.

Mixtures of surfactants can be used e.g. Tween 80/Span 85 mixtures. Acombination of a polyoxyethylene sorbitan ester such as polyoxyethylenesorbitan monooleate (Tween 80) and an octoxynol such ast-octylphenoxypolyethoxyethanol (Triton X-100) is also suitable. Anotheruseful combination comprises laureth 9 plus a polyoxyethylene sorbitanester and/or an octoxynol.

Preferred amounts of surfactants (% by weight) are: polyoxyethylenesorbitan esters (such as Tween 80) 0.01 to 1%, in particular about 0.1%;octyl- or nonylphenoxy polyoxyethanols (such as Triton X-100, or otherdetergents in the Triton series) 0.001 to 0.1%, in particular 0.005 to0.02%; polyoxyethylene ethers (such as laureth 9) 0.1 to 20%, preferably0.1 to 10% and in particular 0.1 to 1% or about 0.5%.

Preferred emulsion adjuvants have an average droplets size of <1 μm e.g.≦750 nm, ≦500 nm, ≦400 nm, ≦300 nm, ≦250 nm, ≦220 nm, ≦200 nm, orsmaller. These droplet sizes can conveniently be achieved by techniquessuch as microfluidisation.

Specific oil-in-water emulsion adjuvants useful with the inventioninclude, but are not limited to:

-   -   A submicron emulsion of squalene, Tween 80, and Span 85. The        composition of the emulsion by volume can be about 5% squalene,        about 0.5% polysorbate 80 and about 0.5% Span 85. In weight        terms, these ratios become 4.3% squalene, 0.5% polysorbate 80        and 0.48% Span 85. This adjuvant is known as ‘MF59’ [37-39], as        described in more detail in Chapter 10 of ref. 40 and chapter 12        of ref. 41. The MF59 emulsion advantageously includes citrate        ions e.g. 10 mM sodium citrate buffer.    -   An emulsion of squalene, a tocopherol, and Tween 80. The        emulsion may include phosphate buffered saline. It may also        include Span 85 (e.g. at 1%) and/or lecithin. These emulsions        may have from 2 to 10% squalene, from 2 to 10% tocopherol and        from 0.3 to 3% Tween 80, and the weight ratio of        squalene:tocopherol is preferably ≦1 as this provides a more        stable emulsion. Squalene and Tween 80 may be present volume        ratio of about 5:2. One such emulsion can be made by dissolving        Tween 80 in PBS to give a 2% solution, then mixing 90 ml of this        solution with a mixture of (5 g of DL-α-tocopherol and 5 ml        squalene), then microfluidising the mixture. The resulting        emulsion may have submicron oil droplets e.g. with an average        diameter of between 100 and 250 nm, preferably about 180 nm.    -   An emulsion of squalene, a tocopherol, and a Triton detergent        (e.g. Triton X-100). The emulsion may also include a 3d-MPL (see        below). The emulsion may contain a phosphate buffer.    -   An emulsion comprising a polysorbate (e.g. polysorbate 80), a        Triton detergent (e.g. Triton X-100) and a tocopherol (e.g. an        α-tocopherol succinate). The emulsion may include these three        components at a mass ratio of about 75:11:10 (e.g. 750 μg/ml        polysorbate 80, 110 μg/ml Triton X-100 and 100 μg/ml        α-tocopherol succinate), and these concentrations should include        any contribution of these components from antigens. The emulsion        may also include squalene. The emulsion may also include a        3d-MPL (see below). The aqueous phase may contain a phosphate        buffer.    -   An emulsion of squalane, polysorbate 80 and poloxamer 401        (“Pluronic™ L121”). The emulsion can be formulated in phosphate        buffered saline, pH 7.4. This emulsion is a useful delivery        vehicle for muramyl dipeptides, and has been used with        threonyl-MDP in the “SAF-1” adjuvant [42] (0.05-1% Thr-MDP, 5%        squalane, 2.5% Pluronic L121 and 0.2% polysorbate 80). It can        also be used without the Thr-MDP, as in the “AF” adjuvant [43]        (5% squalane, 1.25% Pluronic L121 and 0.2% polysorbate 80).        Microfluidisation is preferred.    -   An emulsion comprising squalene, an aqueous solvent, a        polyoxyethylene alkyl ether hydrophilic nonionic surfactant        (e.g. polyoxyethylene (12) cetostearyl ether) and a hydrophobic        nonionic surfactant (e.g. a sorbitan ester or mannide ester,        such as sorbitan monoleate or ‘Span 80’). The emulsion is        preferably thermoreversible and/or has at least 90% of the oil        droplets (by volume) with a size less than 200 nm [44]. The        emulsion may also include one or more of: alditol; a        cryoprotective agent (e.g. a sugar, such as dodecylmaltoside        and/or sucrose); and/or an alkylpolyglycoside. Such emulsions        may be lyophilized.    -   An emulsion of squalene, poloxamer 105 and Abil-Care [45]. The        final concentration (weight) of these components in adjuvanted        vaccines are 5% squalene, 4% poloxamer 105 (pluronic polyol) and        2% Abil-Care 85 (Bis-PEG/PPG-16/16 PEG/PPG-16/16 dimethicone;        caprylic/capric triglyceride).    -   An emulsion having from 0.5-50% of an oil, 0.1-10% of a        phospholipid, and 0.05-5% of a non-ionic surfactant. As        described in reference 46, preferred phospholipid components are        phosphatidylcholine, phosphatidylethanolamine,        phosphatidylserine, phosphatidylinositol, phosphatidylglycerol,        phosphatidic acid, sphingomyelin and cardiolipin. Submicron        droplet sizes are advantageous.    -   A submicron oil-in-water emulsion of a non-metabolisable oil        (such as light mineral oil) and at least one surfactant (such as        lecithin, Tween 80 or Span 80). Additives may be included, such        as QuilA saponin, cholesterol, a saponin-lipophile conjugate        (such as GPI-0100, described in reference 47, produced by        addition of aliphatic amine to desacylsaponin via the carboxyl        group of glucuronic acid), dimethyidioctadecylammonium bromide        and/or N,N-dioctadecyl-N,N-bis (2-hydroxyethyl)propanediamine.    -   An emulsion in which a saponin (e.g. QuilA or QS21) and a sterol        (e.g. a cholesterol) are associated as helical micelles [48].    -   An emulsion comprising a mineral oil, a non-ionic lipophilic        ethoxylated fatty alcohol, and a non-ionic hydrophilic        surfactant (e.g. an ethoxylated fatty alcohol and/or        polyoxyethylene-polyoxypropylene block copolymer) [49].    -   An emulsion comprising a mineral oil, a non-ionic hydrophilic        ethoxylated fatty alcohol, and a non-ionic lipophilic surfactant        (e.g. an ethoxylated fatty alcohol and/or        polyoxyethylene-polyoxypropylene block copolymer) [49].

In some embodiments an emulsion may be mixed with antigenextemporaneously, at the time of delivery, and thus the adjuvant andantigen may be kept separately in a packaged or distributed vaccine,ready for final formulation at the time of use. In other embodiments anemulsion is mixed with antigen during manufacture, and thus thecomposition is packaged in a liquid adjuvanted form,. The antigen willgenerally be in an aqueous form, such that the vaccine is finallyprepared by mixing two liquids. The volume ratio of the two liquids formixing can vary (e.g. between 5:1 and 1:5) but is generally about 1:1.Where concentrations of components are given in the above descriptionsof specific emulsions, these concentrations are typically for anundiluted composition, and the concentration after mixing with anantigen solution will thus decrease.

Where a composition includes a tocopherol, any of the α, β, γ, δ, ε or ξtocopherols can be used, but α-tocopherols are preferred. The tocopherolcan take several forms e.g. different salts and/or isomers. Saltsinclude organic salts, such as succinate, acetate, nicotinate, etc.D-α-tocopherol and DL-α-tocopherol can both be used. Tocopherols areadvantageously included in vaccines for use in elderly patients (e.g.aged 60 years or older) because vitamin E has been reported to have apositive effect on the immune response in this patient group [50]. Theyalso have antioxidant properties that may help to stabilize theemulsions [51]. A preferred α-tocopherol is DL-α-tocopherol, and thepreferred salt of this tocopherol is the succinate. The succinate salthas been found to cooperate with TNF-related ligands in vivo.

C. Saponin Formulations [Chapter 22 of Ref 32]

Saponin formulations may also be used as adjuvants in the invention.Saponins are a heterogeneous group of sterol glycosides and triterpenoidglycosides that are found in the bark, leaves, stems, roots and evenflowers of a wide range of plant species. Saponin from the bark of theQuillaia saponaria Molina tree have been widely studied as adjuvants.Saponin can also be commercially obtained from Smilax ornata(sarsaprilla), Gypsophilla paniculata (brides veil), and Saponariaofficianalis (soap root). Saponin adjuvant formulations include purifiedformulations, such as QS21, as well as lipid formulations, such asISCOMs. QS21 is marketed as Stimulon™.

Saponin compositions have been purified using HPLC and RP-HPLC. Specificpurified fractions using these techniques have been identified,including QS7, QS 17, QS 18, QS21, QH-A, QH-B and QH-C. Preferably, thesaponin is QS21. A method of production of QS21 is disclosed in ref. 52.Saponin formulations may also comprise a sterol, such as cholesterol[53].

Combinations of saponins and cholesterols can be used to form uniqueparticles called immunostimulating complexs (ISCOMs) [chapter 23 of ref.32]. ISCOMs typically also include a phospholipid such asphosphatidylethanolamine or phosphatidylcholine. Any known saponin canbe used in ISCOMs. Preferably, the ISCOM includes one or more of QuilA,QHA & QHC. ISCOMs are further described in refs. 53-55. Optionally, theISCOMS may be devoid of additional detergent [56].

A review of the development of saponin based adjuvants can be found inrefs. 57 & 58.

D. Virosomes and Virus Like Particles

Virosomes and virus-like particles (VLPs) can also be used as adjuvantsin the invention. These structures generally contain one or moreproteins from a virus optionally combined or formulated with aphospholipid. They are generally non-pathogenic, non-replicating andgenerally do not contain any of the native viral genome. The viralproteins may be recombinantly produced or isolated from whole viruses.These viral proteins suitable for use in virosomes or VLPs includeproteins derived from influenza virus (such as HA or NA), Hepatitis Bvirus (such as core or capsid proteins), Hepatitis E virus, measlesvirus, Sindbis virus, Rotavirus, Foot-and-Mouth Disease virus,Retrovirus, Norwalk virus, human Papilloma virus, HIV, RNA-phages,Qβ-phage (such as coat proteins), GA-phage, fr-phage, AP205 phage, andTy (such as retrotransposon Ty protein p1). VLPs are discussed furtherin refs. 59-64. Virosomes are discussed further in, for example, ref. 65

E. Bacterial or Microbial Derivatives

Adjuvants suitable for use in the invention include bacterial ormicrobial derivatives such as non-toxic derivatives of enterobacteriallipopolysaccharide (LPS), Lipid A derivatives, immunostimulatoryoligonucleotides and ADP-ribosylating toxins and detoxified derivativesthereof.

Non-toxic derivatives of LPS include monophosphoryl lipid A (MPL) and3-O-deacylated MPL (3dMPL). 3dMPL is a mixture of 3 de-O-acylatedmonophosphoryl lipid A with 4, 5 or 6 acylated chains A preferred “smallparticle” form of 3 De-O-acylated monophosphoryl lipid A is disclosed inref. 66. Such “small particles” of 3dMPL are small enough to be sterilefiltered through a 0.22 μm membrane [66]. Other non-toxic LPSderivatives include monophosphoryl lipid A mimics, such as aminoalkylglucosaminide phosphate derivatives e.g. RC-529 [67,68].

Lipid A derivatives include derivatives of lipid A from Escherichia colisuch as OM-174. OM-174 is described for example in refs. 69 & 70.

Immunostimulatory oligonucleotides suitable for use as adjuvants in theinvention include nucleotide sequences containing a CpG motif (adinucleotide sequence containing an unmethylated cytosine linked by aphosphate bond to a guanosine). Double-stranded RNAs andoligonucleotides containing palindromic or poly(dG) sequences have alsobeen shown to be immunostimulatory.

The CpG's can include nucleotide modifications/analogs such asphosphorothioate modifications and can be double-stranded orsingle-stranded. References 71, 72 and 73 disclose possible analogsubstitutions e.g. replacement of guanosine with2′-deoxy-7-deazaguanosine. The adjuvant effect of CpG oligonucleotidesis further discussed in refs. 74-79.

The CpG sequence may be directed to TLR9, such as the motif GTCGTT orTTCGTT [80]. The CpG sequence may be specific for inducing a Th1 immuneresponse, such as a CpG-A ODN, or it may be more specific for inducing aB cell response, such a CpG-B ODN. CpG-A and CpG-B ODNs are discussed inrefs. 81-83. Preferably, the CpG is a CpG-A ODN.

Preferably, the CpG oligonucleotide is constructed so that the 5′ end isaccessible for receptor recognition. Optionally, two CpG oligonucleotidesequences may be attached at their 3′ ends to form “immunomers”. See,for example, refs. 80 & 84-86.

A useful CpG adjuvant is CpG7909, also known as ProMune™ (ColeyPharmaceutical Group, Inc.). Another is CpG 1826. As an alternative, orin addition, to using CpG sequences, TpG sequences can be used [87], andthese oligonucleotides may be free from unmethylated CpG motifs. Theimmunostimulatory oligonucleotide may be pyrimidine-rich. For example,it may comprise more than one consecutive thymidine nucleotide (e.g.TTTT, as disclosed in ref. 87), and/or it may have a nucleotidecomposition with >25% thymidine (e.g. >35%, >40%, >50%, >60%, >80%,etc.). For example, it may comprise more than one consecutive cytosinenucleotide (e.g. CCCC, as disclosed in ref. 87), and/or it may have anucleotide composition with >25% cytosine(e.g. >35%, >40%, >50%, >60%, >80%, etc.). These oligonucleotides may befree from unmethylated CpG motifs. Immunostimulatory oligonucleotideswill typically comprise at least 20 nucleotides. They may comprise fewerthan 100 nucleotides.

A particularly useful adjuvant based around immunostimulatoryoligonucleotides is known as IC-31™ [88]. Thus an adjuvant used with theinvention may comprise a mixture of (i) an oligonucleotide (e.g. between15-40 nucleotides) including at least one (and preferably multiple) CpImotifs (i.e. a cytosine linked to an inosine to form a dinucleotide),and (ii) a polycationic polymer, such as an oligopeptide (e.g. between5-20 amino acids) including at least one (and preferably multiple)Lys-Arg-Lys tripeptide sequence(s). The oligonucleotide may be adeoxynucleotide comprising 26-mer sequence 5′-(IC)₁₃-3′ (SEQ ID NO: 96).The polycationic polymer may be a peptide comprising 11-mer amino acidsequence KLKLLLLLKLK (SEQ ID NO: 97).

Bacterial ADP-ribosylating toxins and detoxified derivatives thereof maybe used as adjuvants in the invention. Preferably, the protein isderived from E. coli (E. coli heat labile enterotoxin “LT”), cholera(“CT”), or pertussis (“PT”). The use of detoxified ADP-ribosylatingtoxins as mucosal adjuvants is described in ref. 89 and as parenteraladjuvants in ref. 90. The toxin or toxoid is preferably in the form of aholotoxin, comprising both A and B subunits. Preferably, the A subunitcontains a detoxifying mutation; preferably the B subunit is notmutated. Preferably, the adjuvant is a detoxified LT mutant such asLT-K63, LT-R72, and LT-G192. The use of ADP-ribosylating toxins anddetoxified derivatives thereof, particularly LT-K63 and LT-R72, asadjuvants can be found in refs. 91-98. A useful CT mutant is or CT-E29H[99]. Numerical reference for amino acid substitutions is preferablybased on the alignments of the A and B subunits of ADP-ribosylatingtoxins set forth in ref 100, specifically incorporated herein byreference in its entirety solely for the purpose of the alignment andamino acid numbering therein.

F. Human Immunomodulators

Human immunomodulators suitable for use as adjuvants in the inventioninclude cytokines, such as interleukins (e.g. IL-1, IL-2, IL-4, IL-5,IL-6, IL-7, IL-12 [101], etc.) [102], interferons (e.g. interferon-γ),macrophage colony stimulating factor, and tumor necrosis factor. Apreferred immunomodulator is IL-12.

G. Bioadhesives and Mucoadhesives

Bioadhesives and mucoadhesives may also be used as adjuvants in theinvention. Suitable bioadhesives include esterified hyaluronic acidmicrospheres [103] or mucoadhesives such as cross-linked derivatives ofpoly(acrylic acid), polyvinyl alcohol, polyvinyl pyrollidone,polysaccharides and carboxymethylcellulose. Chitosan and derivativesthereof may also be used as adjuvants in the invention [104].

H. Microparticles

Microparticles may also be used as adjuvants in the invention.Microparticles (i.e. a particle of ˜100 nm to ˜150 μm in diameter, morepreferably ˜200 nm to ˜30 μm in diameter, and most preferably ˜500 nm to˜10 μm in diameter) formed from materials that are biodegradable andnon-toxic (e.g. a poly(α-hydroxy acid), a polyhydroxybutyric acid, apolyorthoester, a polyanhydride, a polycaprolactone, etc.), withpoly(lactide-co-glycolide) are preferred, optionally treated to have anegatively-charged surface (e.g. with SDS) or a positively-chargedsurface (e.g. with a cationic detergent, such as CTAB).

I. Liposomes (Chapters 13 & 14 of ref 32)

Examples of liposome formulations suitable for use as adjuvants aredescribed in refs. 105-107.

J. Polyoxyethylene Ether and Polyoxyethylene Ester Formulations

Adjuvants suitable for use in the invention include polyoxyethyleneethers and polyoxyethylene esters [108]. Such formulations furtherinclude polyoxyethylene sorbitan ester surfactants in combination withan octoxynol [109] as well as polyoxyethylene alkyl ethers or estersurfactants in combination with at least one additional non-ionicsurfactant such as an octoxynol [110]. Preferred polyoxyethylene ethersare selected from the following group: polyoxyethylene-9-lauryl ether(laureth 9), polyoxyethylene-9-steoryl ether, polyoxytheylene-8-steorylether, polyoxyethylene-4-lauryl ether, polyoxyethylene-35-lauryl ether,and polyoxyethylene-23-lauryl ether.

K. Phosphazenes

A phosphazene, such as poly[di(carboxylatophenoxy)phosphazene] (“PCPP”)as described, for example, in references 111 and 112, may be used.

L. Muramyl Peptides

Examples of muramyl peptides suitable for use as adjuvants in theinvention include N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP),N-acetyl-normuramyl-L-alanyl-D-isoglutamine (nor-MDP), andN-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamineMTP-PE).

M. Imidazoquinolone Compounds

Examples of imidazoquinolone compounds suitable for use adjuvants in theinvention include Imiquimod (“R-837”) [113,114], Resiquimod (“R-848”)[115], and their analogs; and salts thereof (e.g. the hydrochloridesalts). Further details about immunostimulatory imidazoquinolines can befound in references 116 to 120.

N. Substituted Ureas

Substituted ureas useful as adjuvants include compounds of formula I, IIor III, or salts thereof:

as defined in reference 121, such as ‘ER 803058’, ‘ER 803732’, ‘ER804053’, ER 804058’, ‘ER 804059’, ‘ER 804442’, ‘ER 804680’, ‘ER 804764’,ER 803022 or ‘ER 804057’ e.g.:

O. Further Adjuvants

Further adjuvants that may be used with the invention include:

-   -   An aminoalkyl glucosaminide phosphate derivative, such as RC-529        [122,123].    -   A thiosemicarbazone compound, such as those disclosed in        reference 124. Methods of formulating, manufacturing, and        screening for active compounds are also described in        reference 124. The thiosemicarbazones are particularly effective        in the stimulation of human peripheral blood mononuclear cells        for the production of cytokines, such as TNF-α.    -   A tryptanthrin compound, such as those disclosed in        reference 125. Methods of formulating, manufacturing, and        screening for active compounds are also described in        reference 125. The thiosemicarbazones are particularly effective        in the stimulation of human peripheral blood mononuclear cells        for the production of cytokines, such as TNF-α.    -   A nucleoside analog, such as: (a) Isatorabine (ANA-245;        7-thia-8-oxoguanosine):

-   -    and prodrugs thereof; (b) ANA975; (c) ANA-025-1; (d)        ANA380; (e) the compounds disclosed in references 126 to        128Loxoribine (7-allyl-8-oxoguanosine) [129].    -   Compounds disclosed in reference 130, including: Acylpiperazine        compounds, Indoledione compounds, Tetrahydraisoquinoline (THIQ)        compounds, Benzocyclodione compounds, Aminoazavinyl compounds,        Aminobenzimidazole quinolinone (ABIQ) compounds [131,132],        Hydrapthalamide compounds, Benzophenone compounds, Isoxazole        compounds, Sterol compounds, Quinazilinone compounds, Pyrrole        compounds [133], Anthraquinone compounds, Quinoxaline compounds,        Triazine compounds, Pyrazalopyrimidine compounds, and Benzazole        compounds [134].    -   Compounds containing lipids linked to a phosphate-containing        acyclic backbone, such as the TLR4 antagonist E5564 [135,136]:    -   A polyoxidonium polymer [137,138] or other N-oxidized        polyethylene-piperazine derivative.    -   Methyl inosine 5′-monophosphate (“MIMP”) [139].    -   A polyhydroxlated pyrrolizidine compound [140], such as one        having formula:

-   -    where R is selected from the group comprising hydrogen,        straight or branched, unsubstituted or substituted, saturated or        unsaturated acyl, alkyl (e.g. cycloalkyl), alkenyl, alkynyl and        aryl groups, or a pharmaceutically acceptable salt or derivative        thereof. Examples include, but are not limited to: casuarine,        casuarine-6-α-D-glucopyranose, 3-epi-casuarine, 7-epi-casuarine,        3,7-diepi-casuarine, etc.    -   A CD1d ligand, such as an α-glycosylceramide [141-148] (e.g.        α-galactosylceramide), phytosphingosine-containing        α-glycosylceramides, OCH, KRN7000        [(2S,3S,4R)-1-O-(α-D-galactopyranosyl)-2-(N-hexacosanoylamino)-1,3,4-octadecanetriol],        CRONY-101, 3″-O-sulfo-galactosylceramide, etc.    -   A gamma inulin [149] or derivative thereof, such as algammulin.

Adjuvant Combinations

The invention may also comprise combinations of aspects of one or moreof the adjuvants identified above. For example, the following adjuvantcompositions may be used in the invention: (1) a saponin and anoil-in-water emulsion [150]; (2) a saponin (e.g. QS21)+a non-toxic LPSderivative (e.g. 3dMPL) [151]; (3) a saponin (e.g. QS21)+a non-toxic LPSderivative (e.g. 3dMPL)+a cholesterol; (4) a saponin (e.g.QS21)+3dMPL+IL-12 (optionally+a sterol) [152]; (5) combinations of 3dMPLwith, for example, QS21 and/or oil-in-water emulsions [153]; (6) SAF,containing 10% squalane, 0.4% Tween 80™, 5% pluronic-block polymer L121,and thr-MDP, either microfluidized into a submicron emulsion or vortexedto generate a larger particle size emulsion. (7) Ribi™ adjuvant system(RAS), (Ribi Immunochem) containing 2% squalene, 0.2% Tween 80, and oneor more bacterial cell wall components from the group consisting ofmonophosphorylipid A (MPL), trehalose dimycolate (TDM), and cell wallskeleton (CWS), preferably MPL+CWS (Detox™); and (8) one or more mineralsalts (such as an aluminum salt)+a non-toxic derivative of LPS (such as3dMPL).

Other substances that act as immunostimulating agents are disclosed inchapter 7 of ref. 32.

The use of an aluminium hydroxide and/or aluminium phosphate adjuvant isparticularly preferred, and antigens are generally adsorbed to thesesalts. Calcium phosphate is another preferred adjuvant. Other preferredadjuvant combinations include combinations of Th1 and Th2 adjuvants suchas CpG & alum or resiquimod & alum. A combination of aluminium phosphateand 3dMPL may be used.

The compositions of the invention may elicit both a cell mediated immuneresponse as well as a humoral immune response. This immune response willpreferably induce long lasting (e.g. neutralising) antibodies and a cellmediated immunity that can quickly respond upon exposure topnuemococcus.

Two types of T cells, CD4 and CD8 cells, are generally thought necessaryto initiate and/or enhance cell mediated immunity and humoral immunity.CD8 T cells can express a CD8 co-receptor and are commonly referred toas Cytotoxic T lymphocytes (CTLs). CD8 T cells are able to recognized orinteract with antigens displayed on MHC Class I molecules.

CD4 T cells can express a CD4 co-receptor and are commonly referred toas T helper cells. CD4 T cells are able to recognize antigenic peptidesbound to MHC class II molecules. Upon interaction with a MHC class IImolecule, the CD4 cells can secrete factors such as cytokines. Thesesecreted cytokines can activate B cells, cytotoxic T cells, macrophages,and other cells that participate in an immune response. Helper T cellsor CD4+cells can be further divided into two functionally distinctsubsets: TH1 phenotype and TH2 phenotypes which differ in their cytokineand effector function.

Activated TH1 cells enhance cellular immunity (including an increase inantigen-specific CTL production) and are therefore of particular valuein responding to intracellular infections. Activated TH1 cells maysecrete one or more of IL-2, IFN-γ, and TNF-β. A TH1 immune response mayresult in local inflammatory reactions by activating macrophages, NK(natural killer) cells, and CD8 cytotoxic T cells (CTLs). A TH1 immuneresponse may also act to expand the immune response by stimulatinggrowth of B and T cells with IL-12. TH1 stimulated B cells may secreteIgG2a.

Activated TH2 cells enhance antibody production and are therefore ofvalue in responding to extracellular infections. Activated TH2 cells maysecrete one or more of IL-4, IL-5, IL-6, and IL-10. A TH2 immuneresponse may result in the production of IgG1, IgE, IgA and memory Bcells for future protection.

An enhanced immune response may include one or more of an enhanced TH1immune response and a TH2 immune response.

A TH1 immune response may include one or more of an increase in CTLs, anincrease in one or more of the cytokines associated with a TH1 immuneresponse (such as IL-2, IFN-y, and TNF-13), an increase in activatedmacrophages, an increase in NK activity, or an increase in theproduction of IgG2a. Preferably, the enhanced TH1 immune response willinclude an increase in IgG2a production.

A TH1 immune response may be elicited using a TH1 adjuvant. A TH1adjuvant will generally elicit increased levels of IgG2a productionrelative to immunization of the antigen without adjuvant. TH1 adjuvantssuitable for use in the invention may include for example saponinformulations, virosomes and virus like particles, non-toxic derivativesof enterobacterial lipopolysaccharide (LPS), immunostimulatoryoligonucleotides. Immunostimulatory oligonucleotides, such asoligonucleotides containing a CpG motif, are preferred TH1 adjuvants foruse in the invention.

A TH2 immune response may include one or more of an increase in one ormore of the cytokines associated with a TH2 immune response (such asIL-4, IL-5, IL-6 and IL-10), or an increase in the production of IgG1,IgE, IgA and memory B cells. Preferably, the enhanced TH2 immune resonsewill include an increase in IgG 1 production.

A TH2 immune response may be elicited using a TH2 adjuvant. A TH2adjuvant will generally elicit increased levels of IgG1 productionrelative to immunization of the antigen without adjuvant. TH2 adjuvantssuitable for use in the invention include, for example, mineralcontaining compositions, oil-emulsions, and ADP-ribosylating toxins anddetoxified derivatives thereof. Mineral containing compositions, such asaluminium salts are preferred TH2 adjuvants for use in the invention.

Preferably, the invention includes a composition comprising acombination of a TH1 adjuvant and a TH2 adjuvant. Preferably, such acomposition elicits an enhanced TH1 and an enhanced TH2 response, i.e.,an increase in the production of both IgG1 and IgG2a production relativeto immunization without an adjuvant. Still more preferably, thecomposition comprising a combination of a TH1 and a TH2 adjuvant elicitsan increased TH1 and/or an increased TH2 immune response relative toimmunization with a single adjuvant (i.e., relative to immunization witha TH1 adjuvant alone or immunization with a TH2 adjuvant alone).

The immune response may be one or both of a TH1 immune response and aTH2 response. Preferably, immune response provides for one or both of anenhanced TH1 response and an enhanced TH2 response.

The enhanced immune response may be one or both of a systemic and amucosal immune response. Preferably, the immune response provides forone or both of an enhanced systemic and an enhanced mucosal immuneresponse. Preferably the mucosal immune response is a TH2 immuneresponse. Preferably, the mucosal immune response includes an increasein the production of IgA.

E. coli can cause disease at a number of anatomical locations [4] and sothe compositions of the invention may be prepared in various forms. Forexample, the compositions may be prepared as injectables, either asliquid solutions or suspensions. Solid forms suitable for solution in,or suspension in, liquid vehicles prior to injection can also beprepared (e.g. a lyophilised composition or a spray-freeze driedcomposition). The composition may be prepared for topical administratione.g. as an ointment, cream or powder. The composition may be preparedfor oral administration e.g. as a tablet or capsule, as a spray, or as asyrup (optionally flavoured). The composition may be prepared forpulmonary administration e.g. as an inhaler, using a fine powder or aspray. The composition may be prepared as a suppository or pessary. Thecomposition may be prepared for nasal, aural or ocular administratione.g. as drops. The composition may be in kit form, designed such that acombined composition is reconstituted just prior to administration to apatient. Such kits may comprise one or more antigens in liquid form andone or more lyophilised antigens.

Where a composition is to be prepared extemporaneously prior to use(e.g. where a component is presented in lyophilised form) and ispresented as a kit, the kit may comprise two vials, or it may compriseone ready-filled syringe and one vial, with the contents of the syringebeing used to reactivate the contents of the vial prior to injection.

Immunogenic compositions used as vaccines comprise an immunologicallyeffective amount of antigen(s), as well as any other components, asneeded. By ‘immunologically effective amount’, it is meant that theadministration of that amount to an individual, either in a single doseor as part of a series, is effective for treatment or prevention. Thisamount varies depending upon the health and physical condition of theindividual to be treated, age, the taxonomic group of individual to betreated (e.g. non-human primate, primate, etc.), the capacity of theindividual's immune system to synthesise antibodies, the degree ofprotection desired, the formulation of the vaccine, the treatingdoctor's assessment of the medical situation, and other relevantfactors. It is expected that the amount will fall in a relatively broadrange that can be determined through routine trials.

Methods of Treatment, and Administration of the Vaccine

The invention also provides a method for raising an immune response in amammal comprising the step of administering an effective amount of acomposition of the invention. The immune response is preferablyprotective and preferably involves antibodies and/or cell-mediatedimmunity. The method may raise a booster response.

The invention also provides a polypeptide of the invention for use as amedicament e.g. for use in raising an immune response in a mammal.

The invention also provides the use of a polypeptide of the invention inthe manufacture of a medicament for raising an immune response in amammal.

The invention also provides a delivery device pre-filled with animmunogenic composition of the invention.

By raising an immune response in the mammal by these uses and methods,the mammal can be protected against E. coli infection, including ExPECand non-ExPEC strains. The invention is particularly useful forproviding broad protection against pathogenic E. coli, includingintestinal pathotypes such as EPEC, EAEC, EIEC, ETEC and DAECpathotypes. Thus the mammal may be protected against diseases including,but not limited to peritonitis, pyelonephritis, cystitis, endocarditis,prostatitis, urinary tract infections (UTIs), meningitis (particularlyneonatal meningitis), sepsis (or SIRS), dehydration, pneumonia, diarrhea(infantile, travellers', acute, persistent, etc.), bacillary dysentery,hemolytic uremic syndrome (HUS), pericarditis, bacteriuria, etc.

SEQ ID NO: 3 and 12 and their variants are particularly useful forimmunising against the EAEC pathotype, and thus for preventing diarrhea(both acute and chronic).

SEQ ID NO: 3, 12, 199, 109, 115, and 124 and their variants areparticularly useful for immunising against the EAEC pathotype, and thusfor preventing diarrhea (both acute and chronic).

SEQ ID NO: 3, 12, 199, 109, 115, 124, 129, 130, and 131 and theirvariants are particularly useful for immunising against the EAECpathotype, and thus for preventing diarrhea (both acute and chronic).

SEQ ID NO: 4 and 10 and their variants are particularly useful forimmunising against the UPEC pathotype, and thus for preventing UTIsincluding, but not limited to, pyelonephritis, cystitis (both acute andrecurrent), peritonitis, catheter-associated UTIs, prostatisis, andbacteriuria (including asymptomatic bacteriuria).

SEQ ID NO: 4, 10, 101, 107, 116, and 126 and their variants areparticularly useful for immunising against the UPEC pathotype, and thusfor preventing UTIs including, but not limited to, pyelonephritis,cystitis (both acute and recurrent), peritonitis, catheter-associatedUTIs, prostatisis, and bacteriuria (including asymptomatic bacteriuria).

SEQ ID NO: 4, 10, 101, 107, 116, 126, 133, 134, 135, 137, 138, and 139and their variants are particularly useful for immunising against theUPEC pathotype, and thus for preventing UTIs including, but not limitedto, pyelonephritis, cystitis (both acute and recurrent), peritonitis,catheter-associated UTIs, prostatisis, and bacteriuria (includingasymptomatic bacteriuria).

SEQ ID NO: 5 and its variants are particularly useful for immunisingagainst the EIEC pathotype, and thus for preventing dysentery (inparticular bacillary dysentery) and HUS (e.g. in children).

SEQ ID NO: 5, 102, and 117 and their variants are particularly usefulfor immunising against the EIEC pathotype, and thus for preventingdysentery (in particular bacillary dysentery) and HUS (e.g. inchildren).

SEQ ID NO: 6, 9, and 11 and their variants are particularly useful forimmunising against the ETEC pathotype, and thus for preventing diarrhea(including travellers' and infant diarrhea).

SEQ ID NO: 6, 9, 11, 103, 106, 108, 118, 121, and 123 and their variantsare also particularly useful for immunising against the ETEC pathotype,and thus for preventing diarrhea (including travellers' and infantdiarrhea).

SEQ ID NOs: 7, 8, and 16 and their variants are particularly useful forimmunising against the EPEC pathotype, and thus for preventing diarrhea(including infantile diarrhea).

SEQ ID NOs: 7, 8, 16, 104, 105, 113, 119, 120, and 128 and theirvariants are also particularly useful for immunising against the EPECpathotype, and thus for preventing diarrhea (including infantilediarrhea).

The mammal is preferably a human, but may be e.g. a cow, a pig, achicken, a cat or a dog, as E. coli disease is also problematic in thesespecies [4]. Where the vaccine is for prophylactic use, the human ispreferably a child (e.g. a toddler or infant) or a teenager; where thevaccine is for therapeutic use, the human is preferably a teenager or anadult. A vaccine intended for children may also be administered toadults e.g. to assess safety, dosage, immunogenicity, etc.

One way of checking efficacy of therapeutic treatment involvesmonitoring E. coli infection after administration of the compositions ofthe invention. One way of checking efficacy of prophylactic treatmentinvolves monitoring immune responses, systemically (such as monitoringthe level of IgG1 and IgG2a production) and/or mucosally (such asmonitoring the level of IgA production), against the antigens in thecompositions of the invention after administration of the composition.Typically, antigen-specific serum antibody responses are determinedpost-immunisation but pre-challenge whereas antigen-specific mucosalantibody responses are determined post-immunisation and post-challenge.

Another way of assessing the immunogenicity of the compositions of thepresent invention is to express the proteins recombinantly for screeningpatient sera or mucosal secretions by immunoblot and/or microarrays. Apositive reaction between the protein and the patient sample indicatesthat the patient has mounted an immune response to the protein inquestion. This method may also be used to identify immunodominantantigens and/or epitopes within antigens.

The efficacy of vaccine compositions can also be determined in vivo bychallenging animal models of E. coli infection, e.g., guinea pigs ormice, with the vaccine compositions. A murine model of ExPEC and lethalsepsis is described in reference 154. A cotton rat model is disclosed inref. 155

Compositions of the invention will generally be administered directly toa patient. Direct delivery may be accomplished by parenteral injection(e.g. subcutaneously, intraperitoneally, intravenously, intramuscularly,or to the interstitial space of a tissue), or mucosally, such as byrectal, oral (e.g. tablet, spray), vaginal, topical, transdermal ortranscutaneous, intranasal, ocular, aural, pulmonary or other mucosaladministration.

The invention may be used to elicit systemic and/or mucosal immunity,preferably to elicit an enhanced systemic and/or mucosal immunity.

Preferably the enhanced systemic and/or mucosal immunity is reflected inan enhanced TH 1 and/or TH2 immune response. Preferably, the enhancedimmune response includes an increase in the production of IgG 1 and/orIgG2a and/or IgA.

Dosage can be by a single dose schedule or a multiple dose schedule.Multiple doses may be used in a primary immunisation schedule and/or ina booster immunisation schedule. In a multiple dose schedule the variousdoses may be given by the same or different routes e.g. a parenteralprime and mucosal boost, a mucosal prime and parenteral boost, etc.Multiple doses will typically be administered at least 1 week apart(e.g. about 2 weeks, about 3 weeks, about 4 weeks, about 6 weeks, about8 weeks, about 10 weeks, about 12 weeks, about 16 weeks, etc.).

Vaccines of the invention may be used to treat both children and adults.Thus a human patient may be less than 1 year old, 1-5 years old, 5-15years old, 15-55 years old, or at least 55 years old. Preferred patientsfor receiving the vaccines are the elderly (e.g. ≧50 years old, ≧60years old, and preferably ≧65 years), the young (e.g. ≦5 years old),hospitalised patients, healthcare workers, armed service and militarypersonnel, pregnant women, the chronically ill, or immunodeficientpatients. The vaccines are not suitable solely for these groups,however, and may be used more generally in a population.

Vaccines of the invention are particularly useful for patients who areexpecting a surgical operation, or other hospital in-patients. They arealso useful in patients who will be catheterized. They are also usefulin adolescent females (e.g. aged 11-18) and in patients with chronicurinary tract infections.

Vaccines of the invention may be administered to patients atsubstantially the same time as (e.g. during the same medicalconsultation or visit to a healthcare professional or vaccinationcentre) other vaccines e.g. at substantially the same time as a measlesvaccine, a mumps vaccine, a rubella vaccine, a MMR vaccine, a varicellavaccine, a MMRV vaccine, a diphtheria vaccine, a tetanus vaccine, apertussis vaccine, a DTP vaccine, a conjugated H. influenzae type bvaccine, an inactivated poliovirus vaccine, a hepatitis B virus vaccine,a meningococcal conjugate vaccine (such as a tetravalent A-C-W135-Yvaccine), a respiratory syncytial virus vaccine, etc.

Nucleic Acid Immunisation

The immunogenic compositions described above include polypeptideantigens. In all cases, however, the polypeptide antigens can bereplaced by nucleic acids (typically DNA) encoding those polypeptides,to give compositions, methods and uses based on nucleic acidimmunisation. Nucleic acid immunisation is now a developed field (e.g.see references 156 to 163 etc.).

The nucleic acid encoding the immunogen is expressed in vivo afterdelivery to a patient and the expressed immunogen then stimulates theimmune system. The active ingredient will typically take the form of anucleic acid vector comprising: (i) a promoter; (ii) a sequence encodingthe immunogen, operably linked to the promoter; and optionally (iii) aselectable marker. Preferred vectors may further comprise (iv) an originof replication; and (v) a transcription terminator downstream of andoperably linked to (ii). In general, (i) & (v) will be eukaryotic and(iii) & (iv) will be prokaryotic.

Preferred promoters are viral promoters e.g. from cytomegalovirus (CMV).The vector may also include transcriptional regulatory sequences (e.g.enhancers) in addition to the promoter and which interact functionallywith the promoter. Preferred vectors include the immediate-early CMVenhancer/promoter, and more preferred vectors also include CMV intron A.The promoter is operably linked to a downstream sequence encoding animmunogen, such that expression of the immunogen-encoding sequence isunder the promoter's control.

Where a marker is used, it preferably functions in a microbial host(e.g. in a prokaryote, in a bacteria, in a yeast). The marker ispreferably a prokaryotic selectable marker (e.g. transcribed under thecontrol of a prokaryotic promoter). For convenience, typical markers areantibiotic resistance genes.

The vector of the invention is preferably an autonomously replicatingepisomal or extrachromosomal vector, such as a plasmid.

The vector of the invention preferably comprises an origin ofreplication. It is preferred that the origin of replication is active inprokaryotes but not in eukaryotes.

Preferred vectors thus include a prokaryotic marker for selection of thevector, a prokaryotic origin of replication, but a eukaryotic promoterfor driving transcription of the immunogen-encoding sequence. Thevectors will therefore (a) be amplified and selected in prokaryotichosts without polypeptide expression, but (b) be expressed in eukaryotichosts without being amplified. This arrangement is ideal for nucleicacid immunization vectors.

The vector of the invention may comprise a eukaryotic transcriptionalterminator sequence downstream of the coding sequence. This can enhancetranscription levels. Where the coding sequence does not have its own,the vector of the invention preferably comprises a polyadenylationsequence. A preferred polyadenylation sequence is from bovine growthhormone.

The vector of the invention may comprise a multiple cloning site

In addition to sequences encoding the immunogen and a marker, the vectormay comprise a second eukaryotic coding sequence. The vector may alsocomprise an IRES upstream of said second sequence in order to permittranslation of a second eukaryotic polypeptide from the same transcriptas the immunogen. Alternatively, the immunogen-coding sequence may bedownstream of an IRES.

The vector of the invention may comprise unmethylated CpG motifs e.g.unmethylated DNA sequences which have in common a cytosine preceding aguanosine, flanked by two 5′ purines and two 3′ pyrimidines. In theirunmethylated form these DNA motifs have been demonstrated to be potentstimulators of several types of immune cell.

Vectors may be delivered in a targeted way. Receptor-mediated DNAdelivery techniques are described in, for example, references 164 to169. Therapeutic compositions containing a nucleic acid are administeredin a range of about 100 ng to about 200 mg of DNA for localadministration in a gene therapy protocol. Concentration ranges of about500 ng to about 50 mg, about 1 μg to about 2 mg, about 5 μg to about 500μg, and about 20 μg to about 100 μg of DNA can also be used during agene therapy protocol. Factors such as method of action (e.g. forenhancing or inhibiting levels of the encoded gene product) and efficacyof transformation and expression are considerations which will affectthe dosage required for ultimate efficacy. Where greater expression isdesired over a larger area of tissue, larger amounts of vector or thesame amounts re-administered in a successive protocol ofadministrations, or several administrations to different adjacent orclose tissue portions may be required to effect a positive therapeuticoutcome. In all cases, routine experimentation in clinical trials willdetermine specific ranges for optimal therapeutic effect.

Vectors can be delivered using gene delivery vehicles. The gene deliveryvehicle can be of viral or non-viral origin (see generally references170 to 173).

Viral-based vectors for delivery of a desired nucleic acid andexpression in a desired cell are well known in the art. Exemplaryviral-based vehicles include, but are not limited to, recombinantretroviruses (e.g. references 174 to 184), alphavirus-based vectors(e.g. Sindbis virus vectors, Semliki forest virus (ATCC VR-67; ATCCVR-1247), Ross River virus (ATCC VR-373; ATCC VR-1246) and Venezuelanequine encephalitis virus (ATCC VR-923; ATCC VR-1250; ATCC VR 1249; ATCCVR-532); hybrids or chimeras of these viruses may also be used),poxvirus vectors (e.g. vaccinia, fowlpox, canarypox, modified vacciniaAnkara, etc.), adenovirus vectors, and adeno-associated virus (AAV)vectors (e.g. see refs. 185 to 190). Administration of DNA linked tokilled adenovirus [191] can also be employed.

Non-viral delivery vehicles and methods can also be employed, including,but not limited to, polycationic condensed DNA linked or unlinked tokilled adenovirus alone [e.g. 191], ligand-linked DNA [192], eukaryoticcell delivery vehicles cells [e.g. refs. 193 to 197] and nucleic chargeneutralization or fusion with cell membranes. Naked DNA can also beemployed. Exemplary naked DNA introduction methods are described inrefs. 198 and 199. Liposomes (e g. immunoliposomes) that can act as genedelivery vehicles are described in refs. 200 to 204. Additionalapproaches are described in references 205 & 206.

Further non-viral delivery suitable for use includes mechanical deliverysystems such as the approach described in ref. 206. Moreover, the codingsequence and the product of expression of such can be delivered throughdeposition of photopolymerized hydrogel materials or use of ionizingradiation [e.g. refs. 207 & 208]. Other conventional methods for genedelivery that can be used for delivery of the coding sequence include,for example, use of hand-held gene transfer particle gun [209] or use ofionizing radiation for activating transferred genes [207 & 208].

Delivery DNA using PLG {poly(lactide-co-glycolide)} microparticles is aparticularly preferred method e.g. by adsorption to the microparticles,which are optionally treated to have a negatively-charged surface (e.g.treated with SDS) or a positively-charged surface (e.g. treated with acationic detergent, such as CTAB).

Reference 5 and Disclaimers

In some embodiments, the invention may not encompass the use of apolypeptide encoded by SEQ ID NO: 1 e.g. it does not encompass the useof a polypeptide comprising amino acid sequence SEQ ID NO: 2, or it doesnot encompass the use of a polypeptide having N-terminal sequence SEQ IDNO: 98. Such polypeptides, and their coding sequences, are disclosed inreference 5 for use in immunising against NMEC infections.

In other embodiments, however, the polypeptides of reference 5 areencompassed, but e.g. for new medical purposes. As disclosed herein, theclose homology between different E. coli pathotypes means that an immuneresponse against a NMEC-derived polypeptide may provide cross-protectionagainst non-NMEC strains. Thus, when the invention relates to thetreatment or prophylaxis of diseases caused by E. coli strains that arenot in the NMEC pathotype (e.g. against APEC, UPEC or SEPEC strains ofExPEC; or against intestinal E. coli pathotypes, such as EPEC, EAEC,EIEC, ETEC or DAEC strains) then the polypeptides of reference 5 may beencompassed.

Antibodies

Antibodies against E. coli antigens can be used for passive immunisation[210].Thus the invention provides an antibody that binds to at least 2(e.g. to 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or all 13) of the 13 proteinsthat consist each of SEQ ID NOs: 3 to 16. Thus the invention provides anantibody that binds to at least 2 (e.g. to 3, 4, 5, 6, 7, 8, 9, 10, 11,12 or all 13) of the 13 proteins that consist each of SEQ ID NOs: 3 to16, SEQ ID NOs 99-113, and SEQ ID NOs 114-128. Antibodies that bind toonly one of said group of 13 proteins are not encompassed by the presentinvention. Thus the invention provides an antibody that binds to atleast 2 (e.g. to 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or all17) of the 17 proteins that consist each of SEQ ID NOs: 3 to 16, 129,133, 137 and 141, SEQ ID NOs 99-113, 130, 134, 138 and 142, and SEQ IDNOs 114-128, 131, 135, 139 and 143. In certain embodiments, at least oneof the at least 2 or more proteins to which the antibody binds must beselected from one of the four proteins that consist of each of SEQ IDNOs: 129, 133, 137 and 141, SEQ ID NOs 130, 134, 138 and 142, and SEQ IDNOs 131, 135, 139 and 143. Antibodies that bind to only one of saidgroup of 17 proteins are not encompassed by the present invention.

The invention also provides the use of such antibodies in therapy. Theinvention also provides the use of such antibodies in the manufacture ofa medicament. The invention also provides a method for treating a mammalcomprising the step of administering an effective amount of a antibodyof the invention. As described above for immunogenic compositions, thesemethods and uses allow a mammal to be protected against E. coliinfection.

The term “antibody” includes intact immunoglobulin molecules, as well asfragments thereof which are capable of binding an antigen. These includehybrid (chimeric) antibody molecules [211, 212]; F(ab′)2 and F(ab)fragments and Fv molecules; non-covalent heterodimers [213, 214];single-chain Fv molecules (sFv) [215]; dimeric and trimeric antibodyfragment constructs; minibodies [216, 217]; humanized antibody molecules[218-220]; and any functional fragments obtained from such molecules, aswell as antibodies obtained through non-conventional processes such asphage display. Preferably, the antibodies are monoclonal antibodies.Methods of obtaining monoclonal antibodies are well known in the art.Humanised or fully-human antibodies are preferred.

General

The practice of the present invention will employ, unless otherwiseindicated, conventional methods of chemistry, biochemistry, molecularbiology, immunology and pharmacology, within the skill of the art. Suchtechniques are explained fully in the literature. See, e.g., references221-228, etc.

The term “comprising” encompasses “including” as well as “consisting”e.g. a composition “comprising” X may consist exclusively of X or mayinclude something additional e.g. X+Y.

The term “about” in relation to a numerical value x means, for example,x±10%.

“GI” numbering is used herein. A GI number, or “GenInfo Identifier”, isa series of digits assigned consecutively to each sequence recordprocessed by NCBI when sequences are added to its databases. The GInumber bears no resemblance to the accession number of the sequencerecord. When a sequence is updated (e.g. for correction, or to add moreannotation or information) then it receives a new GI number. Thus thesequence associated with a given GI number is never changed:

References to a percentage sequence identity between two amino acidsequences means that, when aligned, that percentage of amino acids arethe same in comparing the two sequences. This alignment and the percenthomology or sequence identity can be determined using software programsknown in the art, for example those described in section 7.7.18 of ref.229. A preferred alignment is determined by the Smith-Waterman homologysearch algorithm using an affine gap search with a gap open penalty of12 and a gap extension penalty of 2, BLOSUM matrix of 62. TheSmith-Waterman homology search algorithm is disclosed in ref. 230.

One of skill in the art would understand that “isolated” means altered“by the hand of man” from its natural state, i.e., if it occurs innature, it has been changed or removed from its original environment, orboth. For example, a polynucleotide or a polypeptide naturally presentin a living organism is not “isolated” when in such living organism, butthe same polynucleotide or polypeptide separated from the coexistingmaterials of its natural state is “isolated,” as the term is used inthis disclosure. Further, a polynucleotide or polypeptide that isintroduced into an organism by transformation, genetic manipulation orby any other recombinant method would be understood to be “isolated”even if it is still present in said organism, which organism may beliving or non-living, except where such transformation, geneticmanipulation or other recombinant method produces an organism that isotherwise indistinguishable from the naturally occurring organism.

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1 shows a CLUSTALW alignment of SEQ ID NOs: 2 to 16. The N-terminalregions that may be removed to increase solubility while maintainingsubstantially the same immunogenicity are shown at the bottom of thealignment. The N-terminal region up to the gly-ser linker or gly-serregion is denoted with “G” and the proline-rich region is denoted with“P.”

FIG. 2 shows the amino acid identity between pairs of sequences.

FIG. 3 shows gel analysis of purified protein, with high MW bandsvisible in the absence of DTT.

FIG. 4 shows the Western Blot of pathogenic and non pathogenic E. colistrains using an anti-AcfD serum. Panel (A) is a Western Blot of thetotal cell lysate. Panel (B) is a Western Blot of the supernatant fromthe culture. The lanes in each of panel (A) and (B) from left to rightare as follows: Lane M—marker proteins with the molecular weight in kDaof each marker protein shown along the left side of panel (A);1—IHE3034; 2—CFT073; 3—536; 4—BL21; 5—MG 1655; 6—W3110; 7—NISSLE1917;8—IHE3034ΔActD. As observed from the analysis, pathogenic strains(IHE3034, lane 1; 536, lane 3) express and secrete AcfD whilenon-pathogenic strains (MG1655, lane 5; W3110, lane 6; Nissle 1917, lane7) express the protein but its secretion is defective. Strains CFT073(lane 2) and IHE3034DAcfD (lane 8) are used as negative control, sincethey don't harbor the acfD gene. BL21 strain (lane 4) is a lab strainused as positive control, since it expresses and secretes AcfD.

FIG. 5 shows a comparison of solubility of the AcfD protein and variousfragments of the protein. Panel (A) is an SDS-PAGE gradient gel (4-12%MOPS buffer) of samples at 37° C. comparing the pellet (left lane foreach protein or fragment) to the supernatant (right lane for eachprotein or fragment. The lanes from left to right are: Molecular weightmarkers (191 kDa, 97 kDa and 64 kDa bands are labelled), controlbacteria transformed with the pET expression vector with no insert,bacterial expression of 3526 (his tag+leader peptide removed), bacterialexpression of L3526 (his tag+full length), bacterial expression ofL3526-2stop (full length), bacterial expression of 3526-DG (histag+removal of the N-terminus of AcfD to the flexible glycine-serinelinker), and bacterial expression of 3526-DP (his tag+removal of theN-terminus of AcfD through the proline rich region). Panel (B) is anSDS-PAGE gradient gel (4-12% MOPS buffer) of samples at 25° C. followingthe same order for the lanes as panel (A).

FIG. 6 shows a comparison of expression and purification of the AcfDprotein and various fragments of the protein. Panel (A) is an SDS-PAGEgel (12% MOPS buffer) of samples at from bacteria expressing 3526 (histag+leader peptide removed), cultured a 25° C. comparing factions fromvarious stages of the purification. The lanes from left to right are: M:Molecular weight markers (191 kDa, 97 kDa and 64 kDa bands arelabelled), TOT: total bacterial lysate, INS: insoluble fraction ofbacterial lysate, SM: soluble fraction of bacterial lysate, FT: flowthrough from Nickel column; E1, E2, and E3 three eltions with 500 mMimidazole buffer. Panel (B) is an SDS-PAGE gel (12% MOPS buffer) ofsamples at from bacteria expressing ΔG3526 (his tag+removal of theN-terminus of AcfD to the flexible glycine-serine linker) cultured a 25°C. comparing factions from various stages of the purification. The lanesfrom left to right are: M: Molecular weight markers (191 kDa, 97 kDa and64 kDa bands are labelled), TOT: total bacterial lysate, INS: insolublefraction of bacterial lysate, SM: soluble fraction of bacterial lysate,FT: flow through from Nickel column; E1, E2, and E3 three eltions with500 mM imidazole buffer. Panel (C) is an SDS-PAGE gel (12% MOPS buffer)of samples at from bacteria expressing ΔP3526 (his tag+removal of theN-terminus of AcfD through the proline rich region), cultured a 25° C.comparing factions from various stages of the purification. The lanesfrom left to right are: M: Molecular weight markers (191 kDa, 97 kDa and64 kDa bands are labelled), TOT: total bacterial lysate, INS: insolublefraction of bacterial lysate, SM: soluble fraction of bacterial lysate,FT: flow through from Nickel column; E1, E2, and E3 three elutions with500 mM imidazole buffer.

FIG. 7 shows the amino acid identity between additional pairs ofsequences. Sixteen Enterohemorrhagic E. coli (EHEC) were not found tohave AcfD genes (not shown). The sequences (where represented) from leftto right or top to bottom are as follows: 10 non-pathogenic or commensalstrains (1: a commensal E. coli strain, 2: DH10B strain, 3: MG1655strain, 4: W3110 strain (SEQ ID NO:14); 5: HS strain (SEQ ID NO:13); 9:another commensal E. coli strain; and 10: yet another commensal E. colistrain); three NMEC strains (1: NMEC strain RS218; 2: NMEC strainIHE3034 (SEQ ID NO:2); and 3: NMEC strain S88 (SEQ ID NO:141)); one APECstrain (1: APEC O1 strain); six UPEC strains (2: UPEC strain 536 (SEQ IDNO:4); 3: UTI89; 4: UPEC strain F11 (SEQ ID NO:10); 5: UPEC strain IA139(SEQ ID NO:133); and 6: UPEC strain UMNO26 (SEQ ID NO:137)); three EAECstrains (1: EAEC strain 101-1 (SEQ ID NO:3); 2: EAEC strain O42 (SEQ IDNO:12; and 3: EAEC strain 55989 (SEQ ID NO:129)); one EIEC strain (1:EIEC strain 53638 (SEQ ID NO:5)); four EPEC strains (2: EPEC strain E22(SEQ ID NO: 8)); 3: EPEC strain E2348/69 (SEQ ID NO:16); and 4: EPECstrain E110019 (SEQ ID NO:7)); three ETEC strains (1: ETEC strain B7A(SEQ ID NO:6); 2: ETEC strain E24377A (SEQ ID NO:9); and 3: ETEC strainH10407 (SEQ ID NO:11)); and one antibiotic resistant strain (1:antibiotic-resistant strain SECEC (SEQ ID NO:15)).

BRIEF DESCRIPTION OF SEQUENCE LISTING SEQ ID Description 1 Codingsequence from NMEC strain IHE3034 2 Sequence from NMEC strain IHE3034 3Sequence from EAEC strain 101-1 (GI: 83587587) 4 Sequence from UPECstrain 536 (GI: 110643204) 5 Sequence from EIEC strain 53638 (GI:75515237) 6 Sequence from ETEC strain B7A (GI: 75227618) 7 Sequence fromEPEC strain E110019 (GI: 75239450) 8 Sequence from EPEC strain E22 (GI:75259912) 9 Sequence from ETEC strain E24377A (GI: 157156747) 10Sequence from UPEC strain F11 (GI: 75241179) 11 Sequence from ETECstrain H10407 12 Sequence from EAEC strain O42 13 Sequence fromcommensal strain HS (GI: 157162442) 14 Sequence from commensal strainW3110 (GI: 89109748) 15 Sequence from antibiotic-resistant strain SECEC16 Sequence from EPEC strain E2348/69 17-95 Fragments common to SEQ IDNOs: 2 to 15 96 IC31 nucleotide 97 IC31 peptide 98 Optionally disclaimedN-terminus sequence  99-113 Representative deletions of the N-terminusof AcfD through the gly-ser linker or gly-ser region 114-128Representative deletion of the N-terminus of AcfD through the prolinerich region 129 Amino acid sequence from EAEC strain 55989 130Representative deletion of the N-terminus of AcfD from EAEC strain 55989through the gly-ser linker or gly-ser region 131 Representative deletionof the N-terminus of AcfD from EAEC strain 55989 through the prolinerich region 132 Nucleic acid sequence from EAEC strain 55989 133 Aminoacid sequence from UPEC strain IAI39 134 Representative deletion of theN-terminus of AcfD from UPEC strain IAI39 through the gly-ser linker orgly-ser region 135 Representative deletion of the N-terminus of AcfDfrom UPEC strain IAI39 through the proline rich region 136 Nucleic acidsequence from UPEC strain IAI39 137 Amino acid sequence from UPEC strainUMN026 138 Representative deletion of the N-terminus of AcfD from UPECstrain UMN026 through the gly-ser linker or gly-ser region 139Representative deletion of the N-terminus of AcfD from UPEC strainUMN026 through the proline rich region 140 Nucleic acid sequence fromUPEC strain UMN026 141 Amino acid sequence from NMEC strain S88 142Representative deletion of the N-terminus of AcfD from NMEC strain S88through the gly-ser linker or gly-ser region 143 Representative deletionof the N-terminus of AcfD from NMEC strain S88 through the proline richregion 144 Nucleic acid sequence from NMEC strain S88

Escherichia coli 55989 (Diarrhea-associated isolate, no plasmid—SEQ IDNOs: 129, 130 (ΔG), 131 (ΔP), and 132): Escherichia coli 55989 is aclinical enteroaggregative isolate. Enteroaggregative E. coli strainsadhere to mucosal cells and are an emerging cause of gastroenteritis.Escherichia coli IA139 (Urinary tract infection isolate, no plasmid SEQID NOs: 133, 134 (ΔG), 135 (ΔP), and 136): Escherichia coli IA139 is aserotype O7:K1 strain from a urinary tract infection. Escherichia coliUMN026 (Urinary tract infection isolate, 1 plasmid—SEQ ID NOs: 137, 138(ΔG), 139 (ΔP), and 140): Escherichia coli UMN026 is a serotype O7:K1clinical isolate. This strain is drug resistant.

Escherichia coli S88 (Meningitis isolate, no plasmid—SEQ ID NOs: 141,142 (ΔG), 143 (ΔP), and 144): Escherichia coli S88 is a serotype O45:K1strain isolated from a case of neonatal meningitis.

MODES FOR CARRYING OUT THE INVENTION

One of the antigens disclosed in reference 5 is annotated as accessorycolonization factor D (AcfD) precursor (amino acid SEQ ID NO: 2 herein)from NMEC strain IHE3034. This protein has been expressed and purified,and it confers protection against ExPEC strains in a sepsis animalmodel.

Sequences were obtained for the orthologs in various other E. colistrains. The amino acid sequence seen in IHE3034 was also seen instrains APECO1 and UTI89, but 14 extra sequences were found (SEQ ID NOs:3 to 16). FIG. 1 shows an alignment of SEQ ID NOs: 2 to 16. There areseveral stretches of conservation across the sequences (SEQ ID NOs: 17to 95). The 30 N-terminal amino acids are 100% conserved, and theseinclude the signal peptide (aa 1-23) and the N-terminus cysteine of thenative lipoprotein.

Some strains had a frameshift mutation in the AcfD gene, resulting in noexpression of the polypeptide. The acfD gene was totally absent fromstrains CFT073, EDL933, Sakai and B171.

FIG. 2 shows the % identity between the amino acid sequences. The labelsare SEQ ID NOs, except for MG1655, RS218, DH10B, APECO1 and UTI89 wherethe strain name is used. The lowest level of identity (boxed in FIG. 2)was 85.9%, between SEQ ID NOs: 2 and 4 (both ExPEC strains).

The AcfD sequence from strain IHE3034 was cloned and then and expressed,from a plasmid as a recombinant His-tagged protein without a leaderpeptide, in an E. coli host. Protein was purified and analysed. Gelfiltration showed a much higher molecular weight than predicted basedsolely on the amino acid sequence. Gel analysis in the absence of DTT,but not in its presence, shows higher molecular weight forms of theprotein (FIG. 3). Thus the protein is likely to form oligomers.

Sera raised against AcfD were used in western blots against total celllysates (FIG. 4(A)) or culture supernatants precipitated with 60% TCA(FIG. 4(B)). The sera recognised a ˜150 kDa protein in lysates from bothpathogenic and commensal strains. They did not react with this band inlysates from CFT073 or from an AcfD knockout mutant of IHE3034.Reactivity with proteins in the supernatants indicates that the proteinmay be secreted.

CD1 mice (5 weeks old) were immunized sub-cutaneously using 20 μg of theantigen plus Freund's adjuvant (or other adjuvant as indicated below).The mice were inoculated at 0, 21, and 35 days. Fourteen days after thethird inoculation, the mice were challenged with a lethal dose (LD80) ofa pathogenic strain of E. coli. Blood was collected from the tail 24hours after challenge to evaluate bacteremia. The mortality wasmonitored for four days post-challenge. The protection rate may becalculated as (% dead in control group (no immunization)−% dead inexperimental group (immunized))/% dead in control group×100.

In further experiments using an aluminium salt adjuvant, to which theprotein adsorbed completely, 75% of mice were protected vs. 0% in thecontrol groups. The deaths in both groups occurred within 1 day oflethal challenge.

In further experiments, the recombinant host was grown under twodifferent pO₂ conditions during expression. Under both conditions theprotein was visible in two pools with a different charge. No significantdifferences were seen in the protective efficacy of the four differentpools of protein.

Increased Solubility

Unexpectedly, AcfD protein displayed low solubility even though theprotein is a secreted protein. As shown in FIG. 5(B), removal of theN-terminus of AcfD through the gly-ser linker or gly-ser regionsignificantly increased solubility when expressed at 25° C. (SeepK1-3526-DG FIG. 5(B)). Similarly removal of the N-terminus of AcfDthrough the proline rich region significantly increased solubility whenexpressed at 25° C. (See pK1-3526-DP FIG. 5(B)).

To confirm that both fragments had substantially the same immunogenicityas the full length AcfD, the fragments were purified. The purifiedfragments were used in three immunization experiments in mice,adjuvanted with Freund's complete adjuvant Immunized mice were thenchallenged with a lethal dose of E. coli. Immunization with AcfD withthe N-terminus through the gly-ser linker or gly-ser region removedprotected 100% of the mice from death, whereas death occurred in 90% ofthe animals in the non-immunized control group. Immunization with AcfDwith the N-terminus through the proline rich region removed protected90% of the mice from death, whereas death occurred in 90% of the animalsin the non-immunized control group.

Expression and Purification

Bacteria with one of the three constructs expressing his-tagged variantsof AcfD were cultured in 30 ml of medium and induced to express the AcfDvariant at 25° C. (AcfD without the leader peptide (3526), AcfD with theN-terminus removed through the gly-ser linker or gly-ser region(ΔG3526), and AcfD with the N-terminus removed through the proline richregion (ΔG3526)). The bacteria was harvested and lysed by sonication.The soluble fractions were isolated and loaded on an IMAC column. Thecolumn was washed three times with 20 mM imidazole buffer. The AcfDvariants were then eluted with three washes of 500 mM imidazole buffer.As shown in FIG. 6, removal of the N-terminus of AcfD through thegly-ser linker or gly-ser region significantly increased solubility andyield of purified protein. The yield obtained was estimated by Bradfordassay to be as follows: 0.18 mg of 3526 and 2.34 mg ΔG3526.

It will be understood that the invention has been described by way ofexample only and modifications may be made whilst remaining within thescope and spirit of the invention.

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1. A polypeptide comprising an amino acid sequence that: (a) isidentical to any one of SEQ ID NOs: 3 to 16; (b) has from 1 to 10 singleamino acid alterations compared to (a); (c) has at least 85% sequenceidentity to any one of SEQ ID NOs: 3 to 16; (d) is a fragment of atleast 10 consecutive amino acids of any of SEQ Ill NOs: 3 to 16; and/or(e) when aligned with any of SEQ ID NOs: 3 to 16 using a pairwisealignment algorithm, each moving window of x amino acids from N-terminusto C-terminus has at least x·y identical aligned amino acids, where x is30 and y is 0.75. provided that said amino acid sequence is not SEQ IDNO:
 2. 2. A polypeptide comprising an amino acid sequence: (a) having atleast 75% identity to any of SEQ ID NOs: 3 to 16; and (b) comprising afragment of at least 10 consecutive amino acids of any of SEQ ID NOs: 3to 16, provided that said amino acid sequence is not SEQ ID NO:
 2. 3.(canceled)
 4. The polypeptide of claim 1, including a Zn²⁺ ion.
 5. An E.coli cell, containing a plasmid that encodes a polypeptide of claim 1.6. An immunogenic polypeptide comprising a fragment of an E. coli AcfDprotein wherein the fragment contains a deletion relative to the E. coliAcfD protein which increases solubility of the fragment as compared tothe full length protein and wherein the fragment raises a substantiallysimilar immune response in a subject as the E. coli AcfD protein.
 7. Theimmunogenic polypeptide of claim 6, wherein the E. coli ACfD protein hasan amino acid sequence selected from the group consisting of SEQ IDNOs:2-16.
 8. (canceled)
 9. The immunogenic polypeptide of claim 6wherein the immunogenic polypeptide fragment comprises an amino acidsequence that comprises: (f) the amino acid sequence selected from thegroup consisting of SEQ ID NOs 99 to 128; (g) from 1 to 10 single aminoacid alterations compared to SEQ ID NOs: 99 to 128; (h) at least 85%sequence identity to any one of SEQ ID NOs: 99 to 128; (i) a fragment ofat least 10 consecutive amino acids of any of SEQ ID NOs: 99 to 128;and/or (j) when aligned with any of SEQ ID NOs: 99 to 128 using apairwise alignment algorithm, each moving window of x amino acids from Nterminus to C terminus has at least x·y identical aligned amino acids,where x is 30 and y is 0.75.
 10. (canceled)
 11. (canceled)
 12. Theimmunogenic polypeptide of claim 9 wherein the immunogenic polypeptidefragment is isolated, purified, or recombinant.
 13. The immunogenicpolypeptide of claim 9 further comprising an adjuvant.
 14. Apolynucleotide encoding the immunogenic polypeptide of claim
 9. 15. AnE. coli cell, containing a plasmid that encodes the immunogenicpolypeptide of claim
 9. 16. The immunogenic polypeptide of claim 6,wherein the deletion is removal of substantially all of the N-terminalamino acids up to the gly-ser region, removal of all or a part of theN-terminal proline-rich repeat, or both.
 17. The immunogenic polypeptideof claims 16 wherein the immunogenic polypeptide fragment comprises anamino acid sequence that comprises: (k) the amino acid sequence selectedfrom the group consisting of SEQ ID NOs 99 to 128; (1) from 1 to 10single amino acid alterations compared to SEQ ID NOs: 99 to 128; (m) atleast 85% sequence identity to any one of SEQ ID NOs: 99 to 128; (n) afragment of at least 10 consecutive amino acids of any of SEQ ID NOs: 99to 128; and/or (o) when aligned with any of SEQ ID NOs: 99 to 128 usinga pairwise alignment algorithm, each moving window of x amino acids fromN terminus to C terminus has at least x·y identical aligned amino acids,where x is 30 and y is 0.75.
 18. The immunogenic polypeptide of claim 17wherein the immunogenic polypeptide fragment is isolated, purified, orrecombinant.
 19. The immunogenic polypeptide of claim 17 furthercomprising an adjuvant.
 20. A polynucleotide encoding the immunogenicpolypeptide of claim
 17. 21. An E. coli cell, containing a plasmid thatencodes the immunogenic polypeptide of claim
 17. 22. An immunogenicpolypeptide comprising a fragment of an E. coli AcfD protein wherein thefragment contains a deletion relative to the E. coli AcfD protein havingan amino acid sequence selected from the group consisting of SEQ ID NOs:129, 133, and 137, which increases solubility of the fragment ascompared to the full length protein and wherein the fragment raises asubstantially similar immune response in a subject as the E. coli AcfDprotein.
 23. (canceled)
 24. (canceled)
 25. The immunogenic polypeptideof claim 22 wherein the immunogenic polypeptide fragment comprises anamino acid sequence that comprises: (p) the amino acid sequence selectedfrom the group consisting of SEQ ID NOs 130, 131, 134, 135, 138, and139; (q) from 1 to 10 single amino acid alterations compared to SEQ IDNOs: 130, 131, 134, 135, 138, and 139; (r) at least 85% sequenceidentity to any one of SEQ ID NOs: 130, 131, 134, 135, 138, and 139; (s)a fragment of at least 10 consecutive amino acids of any of SEQ ID NOs:130, 131, 134, 135, 138, and 139; and/or (t) when aligned with any ofSEQ ID NOs: 130, 131, 134, 135, 138, and 139 using a pairwise alignmentalgorithm, each moving window of x amino acids from N terminus to Cterminus has at least x·y identical aligned amino acids, where x is 30and y is 0.75.
 26. (canceled)
 27. The immunogenic polypeptide of claim25, wherein the native full length protein is selected from the groupconsisting of the amino acid sequence of SEQ ID NOs:129, 133, and 137.28. The immunogenic polypeptide of claim 25 wherein the immunogenicpolypeptide fragment is isolated, purified, or recombinant.
 29. Theimmunogenic polypeptide of claim 25 further comprising an adjuvant. 30.A polynucleotide encoding the immunogenic polypeptide of claim
 25. 31.An E. coli cell, containing a plasmid that encodes the immunogenicpolypeptide of claim
 25. 32. The method of raising an immune response ina mammal against intestinal or uropathogenic E. coli comprisingadministering to the mammal the polypeptide of claim 1 comprising anamino acid sequence that: